Skills
747 standalone AI agent skills for healthcare
ACC list guidelines
List recent American College of Cardiology (ACC) clinical practice guidelines. Returns ACC-authored guidelines published in JACC and other ACC journals, sorted by date. ACC guidelines cover coronary revascularization, valvular heart disease, chest pain evaluation, cardiac catheterization, and cardiovascular risk assessment.
ADA get standards section
Fetch detailed content from a specific ADA Standards of Care section by PMID. Retrieves the abstract and, when available via PubMed Central (PMC), a full-text snippet. Use ADA_list_standards_sections first to get PMIDs for each section. All ADA Standards sections are freely available in PMC. Returns title, abstract, full text snippet, and links.
ADA list standards sections
List all sections/chapters of the current ADA Standards of Medical Care in Diabetes. The ADA publishes the Standards of Care annually in Diabetes Care as a free supplement. Each section covers a specific clinical topic (e.g., glycemic goals, pharmacologic treatment, cardiovascular risk management, diabetes technology). Returns section titles, numbers, PMIDs, and PMC links. Use year parameter to access specific editions (default: 2026).
ADA search standards
Search ADA (American Diabetes Association) guidelines and publications by topic using PubMed. Searches publications with ADA as corporate author, returning titles, abstracts, PMIDs, and PMC links. Useful for finding ADA recommendations on specific diabetes-related topics such as glycemic targets, insulin therapy, GLP-1 receptor agonists, SGLT2 inhibitors, gestational diabetes, diabetic kidney disease, or diabetes technology.
ADMETAI predict BBB penetrance
Predicts blood-brain barrier (BBB) penetrance for a given list of molecules in SMILES format.
ADMETAI predict bioavailability
Predicts bioavailability endpoints (Bioavailability_Ma, HIA_Hou, PAMPA_NCATS, Caco2_Wang, Pgp_Broccatelli) for a given list of molecules in SMILES format.
ADMETAI predict clearance distribution
Predicts clearance and distribution endpoints (Clearance_Hepatocyte_AZ, Clearance_Microsome_AZ, Half_Life_Obach, VDss_Lombardo, PPBR_AZ) for a given list of molecules in SMILES format.
ADMETAI predict CYP interactions
Predicts CYP enzyme interactions for a given list of molecules in SMILES format.
ADMETAI predict nuclear receptor activity
Predicts nuclear receptor activity endpoints (NR-AR-LBD, NR-AR, NR-AhR, NR-Aromatase, NR-ER-LBD, NR-ER, NR-PPAR-gamma) for a given list of molecules in SMILES format.
ADMETAI predict physicochemical properties
Predicts physicochemical properties (molecular weight, logP, hydrogen bond acceptors/donors, Lipinski, QED, stereo centers, TPSA) for a given list of molecules in SMILES format.
ADMETAI predict solubility lipophilicity hydration
Predicts solubility, lipophilicity, and hydration endpoints (Solubility_AqSolDB, Lipophilicity_AstraZeneca, HydrationFreeEnergy_FreeSolv) for a given list of molecules in SMILES format.
ADMETAI predict stress response
Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of molecules in SMILES format.
ADMETAI predict toxicity
Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, hERG) for a given list of molecules in SMILES format.
ADMETAnalyzerAgent
AI agent that analyzes ADMET data and provides insights on drug-likeness and safety profiles
AdverseEventICDMapper
Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to the most specific ICD-10-CM code.
AdverseEventPredictionQuestionGeneratorWithContext
Generates a set of personalized adverse‐event prediction questions for a given disease and drug, incorporating additional context information such as patient medical history, clinical findings, or research data.
AHA ACC get guideline
Fetch the full text (or a detailed snippet) of a specific AHA (American Heart Association) or ACC (American College of Cardiology) guideline from PubMed Central using its PMID. Returns the abstract and, when the article is open-access in PMC, the full guideline text up to 6000 characters covering recommendations, evidence tables, and rationale. Use AHA_list_guidelines or ACC_list_guidelines first to obtain PMIDs. Many recent AHA/ACC guidelines are open-access in PMC.
AdverseEventPredictionQuestionGenerator
Generates a set of personalized adverse‐event prediction questions for a given disease and drug, across multiple patient subgroups.
AHA list guidelines
List recent American Heart Association (AHA) clinical practice guidelines. Returns AHA-authored guidelines and scientific statements published in Circulation and other AHA journals, sorted by date. Covers cardiovascular guidelines on topics including hypertension, heart failure, cardiac arrest, stroke, arrhythmias, and prevention.
AHA ACC search guidelines
Search AHA (American Heart Association) and ACC (American College of Cardiology) clinical practice guidelines by topic via PubMed. Covers guidelines published in Circulation, JACC, and other AHA/ACC journals. Useful for finding recommendations on hypertension, heart failure, atrial fibrillation, coronary artery disease, valvular heart disease, lipid management, cardiac arrest, and other cardiovascular conditions.
cBioPortal get cancer studies
Get list of cancer studies from cBioPortal
cBioPortal get cancer types
Get all cancer types from cBioPortal including TCGA, Pan-Cancer Atlas, and other studies. Returns cancerTypeId, name, and clinical trial keywords for filtering studies.
cBioPortal get clinical attributes
Get available clinical attributes for a cancer study. Returns attribute IDs, names, and data types. Use to know what clinical data can be queried (e.g., stage, grade, survival).
cBioPortal get gene info
Get detailed information about a specific gene by Entrez Gene ID. Returns gene symbol, aliases, type, and chromosome location.
cBioPortal get gene panel genes
Get all genes in a specific gene panel. Essential for understanding what genes are covered when analyzing mutation frequency data from targeted sequencing studies.
cBioPortal get clinical data
Get clinical data for all samples in a study. Returns patient-level data like tumor stage, histology, survival status. Filter by clinical attribute ID for specific data types.
cBioPortal get gene panels
Get all gene panels used in cBioPortal studies. Gene panels define which genes were sequenced in a study. Use to understand coverage before querying mutation data.
cBioPortal get molecular profiles
Get molecular profiles for a cancer study. Molecular profiles include mutation data, copy number alterations, mRNA expression, etc.
cBioPortal get mutations
Get mutation data for specific genes in a cancer study. This uses the updated cBioPortal API that requires molecular profiles.
cBioPortal get genes
Search for genes by keyword (gene symbol or alias)
cBioPortal get patients
Get all patients in a cancer study
cBioPortal get sample lists
Get all sample lists (cohort definitions) in a cancer study. Sample lists define groups like 'samples with mutations', 'samples with CNA data'. Use for targeted queries.
cBioPortal get samples
Get all samples in a cancer study
cancer biomarkers disease target score
Extract disease-target association scores from cancer biomarkers data. This includes known cancer biomarkers.
cancer gene census disease target score
Extract disease-target association scores from Cancer Gene Census. This provides curated cancer gene data.
CancerPrognosis get gene expression
Fetch gene expression values (RNA-seq) for a specific gene across cancer samples in a TCGA or cBioPortal study. Returns per-sample expression values with summary statistics (mean, median, min, max). Output can be combined with survival data for expression-based prognostic analysis. Supports 33 TCGA cancer types and any cBioPortal study with mRNA expression data.
CancerPrognosis get study summary
Get summary information for a cancer study including available molecular profiles (mutations, expression, CNV), survival-related clinical attributes, and sample counts. Useful for determining what data is available before querying expression or survival data. Lists all 33 supported TCGA cancer type abbreviations.
CancerPrognosis get survival data
Retrieve patient-level overall survival (OS) and disease-free survival (DFS) data from a TCGA or cBioPortal cancer study. Returns per-patient survival times, event status, and age. Data can be directly used with Survival_kaplan_meier or Survival_log_rank_test tools for custom survival analyses. Supports 33 TCGA cancer types (BRCA, LUAD, COAD, GBM, etc.) and 400+ cBioPortal studies.
CancerPrognosis search studies
Search cBioPortal for cancer genomics studies by keyword. Find studies by cancer type, institution, or data type. Returns study IDs that can be used with other CancerPrognosis tools. Covers 400+ studies including all TCGA projects, AACR GENIE, MSK-IMPACT, and institutional cohorts.
cdc data get dataset
Retrieve data from a specific CDC dataset on Data.CDC.gov. Requires a dataset ID (view ID) which can be found using cdc_data_search_datasets.
cdc data search datasets
Search for datasets on Data.CDC.gov (CDC's Socrata-based open data portal). Returns a list of available datasets matching search criteria. Use this to discover datasets before querying data.
ChEMBL get activity
Get detailed information about a specific activity by its activity ID. Activity IDs are found in the results from ChEMBL_search_activities or ChEMBL_get_target_activities.
ChEMBL get assay activities
Get all activity data for an assay by ChEMBL assay ID. Returns bioactivity measurements from the specified assay. To find an assay ID, use ChEMBL_search_assays or ChEMBL_get_target_assays.
ChEMBL get compound record activities
Get all activities for a compound record by compound record ID. Returns bioactivity measurements for the specified compound record.
ChEMBL get compound record
Get compound record information by ChEMBL compound record ID.
ChEMBL get assay
Get detailed information about an assay by its ChEMBL assay ID. To find an assay ID, use ChEMBL_search_assays or ChEMBL_get_target_assays.
ChEMBL get drug mechanisms
Get mechanisms of action for a drug by ChEMBL drug ID or drug name. Accepts drug_chembl_id (e.g., 'CHEMBL1201581') or drug_name (e.g., 'trastuzumab') — drug_name triggers automatic ChEMBL ID lookup.
ChEMBL get drug
Get detailed information about a drug by its ChEMBL drug ID. Includes approval status, indications, and mechanisms. To find a drug ID, use ChEMBL_search_drugs with a drug name.
ChEMBL get molecule image
Get molecular structure image (SVG or PNG format) for a molecule by ChEMBL ID. Returns the image URL and metadata.
ChEMBL get molecule targets
Get all unique targets associated with a molecule by ChEMBL ID. Returns targets that have activity data for the specified molecule (deduplicated from activity records).
ChEMBL get molecule
Get detailed information about a molecule by its ChEMBL ID. Returns molecule properties, structures, synonyms, and related data.
ChEMBL get target activities
Get all activity data for a target by ChEMBL target ID. Returns bioactivity measurements (IC50, Ki, etc.) for molecules tested against this target. Note: activity values may be in different units (nM or uM) depending on the assay — check the 'standard_units' field in each result. To find a target ID, use ChEMBL_search_targets with a target name or gene symbol.
ChEMBL get target assays
Get all assays associated with a target by ChEMBL target ID. To find a target ID, use ChEMBL_search_targets with a target name or gene symbol.
ChEMBL get target
Get detailed information about a target (protein, gene, etc.) by its ChEMBL target ID. To find a target ID, use ChEMBL_search_targets with a target name or gene symbol.
ChEMBL search activities
Search activity data by molecule, target, assay, or activity values. Supports filtering by IC50, Ki, EC50, etc. Note: activity data is sparse and depends on curation; some specific filter combinations can legitimately return zero results. For reliable retrieval, prefer starting from a known target (`target_chembl_id__exact`) or assay (`assay_chembl_id__exact`). To find molecule or target IDs, use ChEMBL_search_molecules or ChEMBL_search_targets.
ChEMBL search assays
Search assays by various criteria including assay type, target, organism. Use this tool to find assay ChEMBL IDs needed for other tools.
ChEMBL search atc classification
Search ATC (Anatomical Therapeutic Chemical) classifications for drugs. To find a drug ID, use ChEMBL_search_drugs.
ChEMBL search binding sites
Search binding sites by target, site name, or other criteria.
ChEMBL search cell lines
Search cell lines used in ChEMBL assays.
ChEMBL search compound structural alerts
Search compound structural alerts (toxicity warnings) by molecule or alert type.
ChEMBL search documents
Search ChEMBL documents (publications) by various criteria.
ChEMBL search drugs
Search drugs by name, approval status, or other criteria. Use the `query` parameter to search by drug name (e.g., {"query": "sotorasib"}). Use `max_phase` to filter by development phase.
ChEMBL search mechanisms
Search mechanisms of action by drug, target, or mechanism type. To find drug or target IDs, use ChEMBL_search_drugs or ChEMBL_search_targets.
ChEMBL search molecules
Search molecules by name, ChEMBL ID, or other criteria. Supports filtering and pagination. Note: some text-based filters (especially `pref_name__contains`) may legitimately return zero results because `pref_name` coverage is incomplete and may not contain common drug names. For reliable retrieval, prefer ID-based filters like `molecule_chembl_id` or use `ChEMBL_get_molecule` when you already have a ChEMBL ID.
ChEMBL search similar molecules
Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the ChEMBL Web Services. Note: This tool is designed for small molecule compounds only. Biologics (antibodies, proteins, oligonucleotides, etc.) do not have SMILES structures and cannot be used for similarity search. For biologics similarity search, use BLAST_protein_search (requires amino acid sequence) or UniProt_search. For small molecules, use PubChem_search_compounds_by_similarity (requires SMILES ...
ChEMBL search protein classification
Search protein classifications by target, classification type, or other criteria. To find a target ID, use ChEMBL_search_targets.
ChEMBL search similarity
Search molecules similar to a given SMILES string using Tanimoto similarity. Returns molecules with similarity above the threshold.
ChEMBL search substructure
Search molecules by substructure using SMILES. Returns molecules containing the specified substructure.
ChEMBL search targets
Search targets by name, organism, target type, or other criteria. Use this tool to find target ChEMBL IDs needed for other tools.
chembl disease target score
Extract disease-target association scores specifically from ChEMBL database. ChEMBL provides bioactivity data for drug-target interactions.
ChEMBL search tissue
Search tissues used in ChEMBL assays.
civic get assertion
Get detailed information about a specific assertion in CIViC database by assertion ID. Assertions are higher-level clinical interpretations that integrate multiple evidence items into formal statements about clinical actionability. Returns assertion description, evidence summary, and associated molecular profile or variant information.
civic get evidence item
Get detailed information about a specific evidence item in CIViC database by evidence ID. Evidence items link molecular profiles or variants to clinical outcomes, therapies, or disease states with curated literature support. Returns evidence description, level (A-E), type (PREDICTIVE, DIAGNOSTIC, PROGNOSTIC), significance, direction, status, disease, therapies, molecular profile, and citation.
civic get molecular profile
Get detailed information about a specific molecular profile in CIViC database by molecular profile ID. Molecular profiles represent combinations of variants or features (e.g., 'BRAF V600E') that serve as biomarkers for clinical interpretation. Returns profile name, description, clinical significance score, and associated evidence items with diseases, therapies, and evidence levels.
civic get variant
Get detailed information about a specific variant in CIViC database by variant ID. Variants represent specific genetic alterations (SNVs, indels, structural variants, etc.) with clinical significance in cancer. Returns variant name, coordinates, gene association, and related information.
civic get variants by gene
Get all variants associated with a specific gene in CIViC database. Returns variant information including names, coordinates, and associated evidence. Use gene_name or gene_symbol (e.g., 'EGFR', 'BRAF') for convenience, or gene_id if already known. Uses cursor-based pagination to return up to 500 variants per call.
civic search assertions
Search for assertions in CIViC database. Assertions are higher-level clinical interpretations that integrate multiple evidence items into formal statements about clinical actionability. Returns a list of assertions with descriptions and associated molecular profiles or variants. Filter by therapy (e.g., 'ponatinib'), disease (e.g., 'leukemia'), or variant name.
civic search diseases
Search for diseases in CIViC database. Returns a list of cancer diseases and conditions (with IDs and names) that are associated with variants and evidence in CIViC. Use 'query' or 'name' to filter by disease name (e.g., 'leukemia', 'melanoma').
civic search evidence items
Search for evidence items in CIViC database. Evidence items are curated statements linking variants or molecular profiles to clinical outcomes, therapies, or disease states. Returns evidence with disease, therapies, significance, direction, and citation. Filter by therapy name (e.g., 'imatinib'), disease name (e.g., 'leukemia'), or molecular profile name (e.g., 'BRAF V600E').
civic search genes
Search for genes in CIViC (Clinical Interpretation of Variants in Cancer) database. CIViC is a community knowledgebase for expert-curated interpretations of variants in cancer. Returns genes with their IDs, names, and descriptions. Use this to find genes of interest before querying variants or evidence.
civic search molecular profiles
Search for molecular profiles in CIViC database. Molecular profiles represent combinations of variants or features (e.g., 'BRAF V600E', 'EGFR T790M') that serve as biomarkers for clinical interpretation. Returns a list of molecular profiles with IDs and names. Use the 'query' parameter to filter by profile name (alias: 'name').
civic search therapies
Search for therapies (drugs/treatments) in CIViC database. Returns a list of cancer therapies and drugs (with IDs and names) that are associated with variants and evidence in CIViC. Use 'query' or 'name' to filter by therapy name (e.g., 'imatinib', 'pembrolizumab').
civic search variants
Search for variants in CIViC database. Returns a list of variants with their IDs and names. Use 'query' to search by variant name (e.g., 'V600E'), or 'gene'/'gene_name' to get all variants for a specific gene (e.g., 'EGFR'). To find a specific variant in a gene, combine gene_name + variant_name (e.g., gene_name='EGFR', variant_name='L858R'). Note: CIViC stores variants without gene prefix — do not combine gene and variant in a single string.
ClinGen get actionability adult
Get ClinGen clinical actionability curations for adult context. Returns genes with actionable findings, intervention scores, and outcome scores. Actionability scores help prioritize which incidental findings to return. Example: BRCA1/2 have high actionability for cancer screening.
ClinGen get actionability pediatric
Get ClinGen clinical actionability curations for pediatric context. Returns genes with actionable findings in children, intervention recommendations, and evidence scores. Pediatric curations may differ from adult context due to age-specific interventions.
ClinGen get dosage sensitivity
Get all ClinGen dosage sensitivity curations. Returns haploinsufficiency and triplosensitivity scores for curated genes. Set include_regions=true to also get recurrent CNV regions. Scores: 0=No evidence, 1=Little, 2=Emerging, 3=Sufficient evidence.
ClinGen get gene validity
Get all ClinGen gene-disease validity curations. Returns comprehensive list of gene-disease relationships with classifications (Definitive, Strong, Moderate, Limited). Useful for batch analysis or exploring curated genes. Optional gene filter available.
ClinGen get variant classifications
Get variant pathogenicity classifications from ClinGen Evidence Repository. Returns expert-curated variant classifications with supporting evidence. Optional filters by gene or variant. Classifications follow ACMG/AMP guidelines with expert review.
ClinGen search actionability
Search ClinGen clinical actionability across both adult and pediatric contexts by gene. Returns actionability data from both contexts for comparison. Useful for comprehensive actionability assessment of a gene across age groups.
ClinGen search dosage sensitivity
Search ClinGen dosage sensitivity curations by gene symbol. Returns haploinsufficiency (HI) and triplosensitivity (TS) scores (0-3 scale). Score 3 = Sufficient evidence for dosage pathogenicity. Critical for CNV interpretation. Example: MECP2 has HI score of 3.
ClinGen search gene validity
Search ClinGen gene-disease validity curations by gene symbol. Returns classification (Definitive, Strong, Moderate, Limited, Disputed, Refuted), disease associations, and inheritance patterns. Essential for ACMG variant classification. Example: BRCA1 returns validity scores for hereditary breast/ovarian cancer.
ClinicalTrialDesignAgent
AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
ClinicalTrials get database stats
Get aggregate statistics about the ClinicalTrials.gov database, including total number of registered studies and size distribution. Returns database-wide counts and file size metrics.
ClinicalTrials get field values
Get value distribution for a specific field across ClinicalTrials.gov studies. Returns all unique values with study counts. Use to see what status, phase, or study type options exist. Example: 'Phase' field returns counts for PHASE1, PHASE2, PHASE3, etc.
ClinicalTrials get study
Get full details for a specific clinical trial by NCT ID from ClinicalTrials.gov. Returns comprehensive protocol including title, objectives, eligibility criteria, interventions, outcome measures, contacts, and results summary. Example: NCT04280705 returns the ACTT remdesivir COVID-19 trial with all details.
ClinicalTrials search by intervention
Search ClinicalTrials.gov for all clinical trials testing a specific drug, biologic, device, or other intervention. Returns trial IDs, titles, phases, status, and conditions being studied. Ideal for finding all trials for a given drug (e.g., 'nivolumab') across all disease indications.
ClinicalTrials search by sponsor
Search ClinicalTrials.gov for clinical trials by sponsor or lead organization. Returns trials funded by pharmaceutical companies, academic institutions, or government agencies. Example: find all Phase 3 trials sponsored by 'National Cancer Institute' for cancer conditions.
ClinicalTrials search studies
Search ClinicalTrials.gov for clinical trial studies by condition, intervention, sponsor, or other criteria. Returns NCT IDs, titles, status, phase, enrollment, and key trial metadata. Example: search for 'breast cancer' trials with 'pembrolizumab' that are RECRUITING in Phase 3.
clinvar get clinical significance
Get clinical significance information for a variant from ClinVar. Returns pathogenicity classification and clinical interpretations.
clinvar get variant details
Get variant summary information from ClinVar by variant ID. Returns accession, title, genes, clinical significance, review status, chromosome location, and variation name. For the same variant, this provides a different field view than clinvar_get_clinical_significance.
clinvar search variants
Search for variants in ClinVar database by gene name, condition, or variant ID. Returns variant identifiers and basic information. At least one of gene, condition, or variant_id must be provided.
CMA Guidelines Search
Search Canadian Medical Association (CMA) Infobase guidelines. Contains over 1200 evidence-based clinical practice guidelines developed or endorsed by Canadian healthcare organizations.
COSMIC get mutations by gene
Get all somatic mutations for a specific gene from COSMIC database. Returns comprehensive mutation data for a gene symbol including CDS changes, amino acid changes, cancer types, and genomic positions. Useful for exploring the mutational landscape of cancer genes like BRAF, TP53, EGFR, KRAS, etc.
CompoundDiscoveryAgent
AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
CPIC get alleles
Get pharmacogenomics alleles and their functional status for a gene from CPIC. Returns allele names, activity values, and functional status. Note: use 'clinicalfunctionalstatus' field for the active clinical classification (e.g., 'No function', 'Normal function'); the 'functionalstatus' field may be null for some genes. Critical for translating genotype to phenotype (e.g., CYP2D6 *4 = no function, CYP2D6 *1 = normal function).
COSMIC search mutations
Search COSMIC database for somatic mutations in cancer. COSMIC is the world's largest expert-curated database of somatic mutations in human cancer. Search by gene name, mutation ID, or mutation description. Returns mutation IDs, gene names, CDS changes, and amino acid changes. No authentication required.
CPIC get drug info
Get pharmacogenomics information for a drug from the CPIC database. Returns drug identifiers including PharmGKB ID, RxNorm, DrugBank, and ATC codes. Use to find pharmacogenomics guidelines for a specific drug. Example drugs: warfarin, codeine, clopidogrel, simvastatin, tamoxifen, fluorouracil, mercaptopurine.
CPIC get gene drug pairs
Get all gene-drug pairs for a pharmacogene from CPIC. Shows which drugs are affected by variants in a specific gene, with CPIC evidence level and PharmGKB clinical annotation level. Evidence levels: A (strongest) to D (weakest). Useful for understanding the clinical significance of a pharmacogene.
CPIC get gene info
Get pharmacogenomics information for a gene from the Clinical Pharmacogenomics Implementation Consortium (CPIC) database. Returns gene coordinates, sequence IDs, and cross-references to PharmGKB, HGNC, NCBI, and Ensembl. Use this to find which genes are pharmacogenomically relevant. Example genes: CYP2D6, CYP2C19, CYP2C9, SLCO1B1, TPMT, DPYD, UGT1A1, VKORC1, G6PD.
CPIC get recommendations
Get drug dosing recommendations from a specific CPIC pharmacogenomic guideline. Returns clinically actionable recommendations that link genotype/phenotype to drug prescribing actions. Each recommendation includes the classification strength (Strong, Moderate, Optional, No recommendation), the drug recommendation text, allele status context, and clinical implications. Use CPIC_list_guidelines first to obtain valid guideline IDs. Key guideline IDs: 100421 (HLA-B/abacavir), 100416 (CYP2D6,OPRM1,...
CPIC list drugs
List all drugs in the CPIC database that have pharmacogenomic annotations. Returns drug names and their associated CPIC guideline IDs. Drugs without a guideline ID have annotations but no full CPIC dosing guideline yet. Use the guidelineid with CPIC_get_recommendations to retrieve dosing recommendations. Covers 100+ drugs including commonly used medications like warfarin, codeine, clopidogrel, simvastatin, tamoxifen, fluorouracil, and abacavir.
CPIC list guidelines
List all CPIC pharmacogenomic guidelines. Returns ~29 evidence-based guidelines (count may vary as guidelines are added/updated) for using pharmacogenomic test results to optimize drug therapy. Each guideline covers one or more gene-drug pairs with specific dosing recommendations based on genotype/phenotype. Includes guideline ID, name, URL, associated genes, and PharmGKB IDs. Use the returned guideline ID with CPIC_get_recommendations to retrieve specific dosing recommendations.
CPIC list pgx genes
List all pharmacogenomics genes curated by the Clinical Pharmacogenomics Implementation Consortium (CPIC). Returns 130+ genes with known drug interactions including CYP enzymes, transporters, and other pharmacogenes. Includes gene coordinates, sequence IDs, and database cross-references.
CPIC search gene drug pairs
Search CPIC gene-drug pairs by gene symbol and/or CPIC evidence level. Gene symbol should be the standard HGNC symbol (e.g., "CYP2D6", "DPYD", "TPMT"). CPIC level indicates evidence strength: A=highest evidence, B=moderate, C=limited, D=for information only. Returns gene-drug pairs with guideline IDs for further lookup.
Crossref get funder
Get detailed metadata for a specific research funder by its Crossref funder ID. Returns comprehensive funder information including official name, alternative names, location, hierarchy (parent organizations), DOI count, and URI. Use this to understand funder details, verify funder identifiers, or explore funding relationships. Find funder IDs using Crossref_list_funders (format: numeric ID like '100000001' for NSF, '100000002' for NIH).
Crossref get journal
Get metadata for a specific journal by its ISSN (International Standard Serial Number). Returns journal details including title, publisher, ISSN variants (print/electronic), coverage dates, and publication frequency. Use this to verify journal information, assess journal credibility for submissions, check publisher details, or validate ISSNs. Find ISSNs from publication metadata or journal databases (format: ####-####).
Crossref get work
Get complete metadata for a specific scholarly work by its DOI (Digital Object Identifier). Returns comprehensive bibliographic information including title, abstract, full author list with affiliations and ORCIDs, journal details, publication dates, volume/issue/pages, references, citations, license, funding information, and related identifiers. Essential for verifying citations, extracting complete metadata, or building reference managers. DOIs can be found using Crossref_search_works (forma...
Crossref list funders
Search and list research funding organizations in the Crossref database. Returns funder details including funder ID, name, location, DOI count, and alternative names. Use this to discover funder identifiers for filtering publications by funding source, or to explore research funding patterns. Essential for grant analysis, funding compliance, or finding publications funded by specific organizations (e.g., NIH, NSF, ERC).
Crossref list types
List all publication types available in Crossref (e.g., journal-article, book-chapter, conference-paper, dataset, preprint). Returns type identifiers and labels. Use this to discover valid publication type filters for Crossref_search_works, understand the classification of research outputs, or analyze publication type distributions. Essential for constructing precise search queries or filtering results by publication category.
Crossref search works
Search Crossref Works API for scholarly articles, publications, and research outputs by keyword. Returns metadata including title, abstract, journal, authors, publication year, DOI, URL, citations, and publisher. Supports filtering by publication type (journal article, conference paper, etc.) and date range. Use this to discover academic literature, verify citations, or build bibliographies. Find DOIs to use with Crossref_get_work for complete metadata.
CTD get chemical diseases
Get curated chemical-disease associations from CTD. Given a chemical name, returns diseases it is associated with, including direct evidence type (therapeutic, marker/mechanism) and disease categories. Example: 'bisphenol A' returns associations with cancer, reproductive disorders, etc.
CTD get chemical gene interactions
Get curated chemical-gene interactions from CTD (Comparative Toxicogenomics Database). Given a chemical name, returns genes it interacts with, including organism, PubMed references, and interaction types. Example: 'bisphenol A' returns thousands of gene interactions across species.
CTD get disease chemicals
Get curated disease-chemical associations from CTD. Given a disease name, returns chemicals associated with it, including evidence type. Example: 'Breast Neoplasms' returns chemicals linked to breast cancer including both therapeutic agents and toxicants.
CTD get gene chemicals
Get curated gene-chemical interactions from CTD. Given a gene symbol, returns chemicals that interact with the gene product, with PubMed evidence. Example: 'TP53' returns over 2000 chemical interactions including drugs, environmental toxicants.
CTD get gene diseases
Get curated gene-disease associations from CTD. Given a gene symbol, returns diseases associated with the gene, including direct evidence and disease categories. Example: 'TP53' returns associations with various cancers and other diseases.
CTFPHC list guidelines
List all published guidelines from the Canadian Task Force on Preventive Health Care (CTFPHC). Fetches the official index of 27 published preventive health guidelines covering cancer screening, cardiovascular risk, diabetes, mental health, and other primary care topics.
CTFPHC search guidelines
Search published guidelines from the Canadian Task Force on Preventive Health Care (CTFPHC) by keyword. Covers preventive health topics including breast cancer, colorectal cancer, diabetes, depression, cognitive impairment, thyroid dysfunction, and more.
DailyMed get spl by setid
Get complete label corresponding to SPL Set ID, returns content in XML or JSON format.
DailyMed parse adverse reactions
Parse adverse reactions section from SPL XML into structured table format. Returns AE frequencies, severity, and descriptions. Example: setid='030d9bca-a934-6ef9-e063-6394a90a8277' extracts headache 10%, GI upset 5%.
DailyMed parse clinical pharmacology
Parse clinical pharmacology section from SPL XML. Returns PK parameters (Cmax, Tmax, t1/2, AUC), PD effects, metabolism pathways, and elimination. Example: absorption, distribution, metabolism tables.
DailyMed parse contraindications
Parse contraindications section from SPL XML into structured list. Returns conditions, populations, or situations where drug should not be used. Example: pregnancy, hypersensitivity, severe renal impairment.
DailyMed parse dosing
Parse dosage and administration section from SPL XML. Returns structured dosing instructions, dose modifications, and administration guidelines. Example: standard dose, dose adjustments for renal/hepatic impairment.
DailyMed parse drug interactions
Parse drug interactions section from SPL XML into structured format. Returns CYP substrates/inhibitors/inducers, P-gp interactions, and specific drug-drug interactions. Example: avoid with strong CYP3A4 inhibitors.
DailyMed search drug classes
Search the DailyMed database for FDA Established Pharmacologic Classes (EPC). Returns drug class names and NDF-RT codes that categorize drugs by their mechanism of action or pharmacologic effect. Use this to find drug classes for a specific therapeutic area (e.g., 'antihypertensive', 'antibiotic', 'antineoplastic') or to look up specific pharmacologic class codes. The drug class codes can be used to search DailyMed_search_spls for all drugs in that class.
DailyMed search spls
Search SPL list using multiple filter conditions (drug_name/ndc/rxcui/setid) and return metadata + data array.
dbsnp get frequencies
Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data.
dbsnp get variant by rsid
Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic variant information.
dbsnp search by gene
Search for variants in a specific gene. Returns variants associated with the gene symbol.
DepMap get cell line
Get detailed metadata for a specific cancer cell line. Returns tissue, cancer type, MSI status, ploidy, mutational burden. Use model_id (e.g., 'SIDM00001') or model_name (e.g., 'A549').
DepMap get cell lines
Get list of cancer cell lines from DepMap/Sanger with metadata. Filter by tissue or cancer type. Returns cell line IDs, tissue, and cancer type for target validation studies.
DepMap get gene dependencies
Get gene dependency information from CRISPR knockout screens. Returns gene IDs and annotations. Negative gene effect scores indicate essentiality (cell death upon knockout).
DepMap search cell lines
Search cancer cell lines by name. Returns matching cell lines with IDs and cancer types. Use for finding cell models by common names (A549, HeLa, MCF7, etc.).
DepMap search genes
Search for genes in DepMap/Sanger by symbol or name. Returns matching genes with Ensembl IDs and exact-match flags. Use this helper to find the correct gene symbol before querying dependencies, especially when DepMap_get_gene_dependencies returns mismatched genes.
DGIdb get drug gene interactions
Get drug-gene interactions for a list of genes from DGIdb. Returns drugs targeting each gene, interaction types, and evidence sources.
DGIdb get drug info
Get basic drug metadata from DGIdb by drug name. Returns drug name, concept ID, and approval status. To get drug-gene interactions, use DGIdb_get_drug_gene_interactions instead.
DGIdb get gene druggability
Get druggability information for genes. Returns gene categories indicating if a gene is druggable (kinase, GPCR, ion channel, etc.).
DGIdb get gene info
Get detailed gene information from DGIdb including aliases, categories, and interaction counts.
DisGeNET get disease genes
Get all genes associated with a disease from DisGeNET. Returns ranked gene list with association scores and evidence counts. Filter by minimum score to get high-confidence associations. Useful for disease gene prioritization.
DisGeNET get gda
Get gene-disease associations with filtering. Filter by data source (CURATED, LITERATURE, ANIMAL_MODELS) and minimum score. Returns comprehensive GDA data with evidence levels. Requires DISGENET_API_KEY.
DisGeNET get vda
Get variant-disease associations from DisGeNET. Query by rsID or gene symbol to find disease-associated variants. Returns variant IDs, diseases, and evidence scores. Useful for pharmacogenomics and variant interpretation.
DisGeNET search disease
Search DisGeNET for genes associated with a disease. Query by disease name or UMLS CUI (e.g., C0006142 for breast cancer). Returns associated genes with scores and evidence. Requires DISGENET_API_KEY.
DisGeNET search gene
Search DisGeNET for diseases associated with a gene. DisGeNET is the largest public database of gene-disease associations. Returns diseases, association scores, and evidence counts. Requires DISGENET_API_KEY env var (register free at disgenet.org).
DiseaseAnalyzerAgent
AI agent that analyzes disease characteristics and identifies potential therapeutic targets using LLM reasoning
disease target score
Extract disease-target association scores from a specific data source using GraphQL API. This tool retrieves all targets associated with a disease and their scores from a specified datasource (e.g., chembl, eva, cancer_gene_census, etc.).
DoseResponse calculate ic50
Determine the half-maximal inhibitory or effective concentration (IC50/EC50) from paired concentration-response data by fitting the Hill sigmoidal equation. Requires a minimum of 4 data points that span the dynamic response range. Output includes EC50 with 95% confidence interval, Hill exponent n, top plateau Emax, bottom plateau Emin, R2 goodness-of-fit, and log10(EC50) for convenient pIC50 conversion. Suited to potency ranking in compound screens, structure-activity relationship analysis, a...
DoseResponse compare potency
Quantify relative potency between two compounds by independently fitting Hill sigmoidal curves to each concentration-response dataset and computing the EC50 fold-shift (compound B EC50 / compound A EC50). Reports EC50, Hill exponent, and plateau Emax per compound, the potency fold-ratio, and which compound is more potent. Applications include lead optimisation, matched-pair structure-activity analysis, and selectivity profiling.
DoseResponse fit curve
Nonlinear regression of paired concentration-response measurements to the Hill sigmoidal (4PL) model: f(x) = Emin + (Emax - Emin) / (1 + (EC50/x)^n). Returns the four fitted parameters (baseline Emin, plateau Emax, midpoint EC50, Hill exponent n) with standard errors, 95% CI for EC50, coefficient of determination R2, and predicted response at each measured concentration. Requires at least 4 positive concentration inputs. Useful for characterising pharmacological potency and assessing assay da...
DrugInteractionAnalyzerAgent
AI agent that analyzes drug-drug interactions and provides clinical recommendations
DrugOptimizationAgent
AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
DrugProps calculate qed
Calculate Quantitative Estimate of Drug-likeness (QED) score for a compound using the Bickerton et al. (2012) method. QED integrates 8 molecular descriptors (MW, AlogP, HBA, HBD, PSA, rotatable bonds, aromatic rings, structural alerts) into a single score from 0 (non-drug-like) to 1 (most drug-like). Median QED of approved oral drugs is ~0.49. High QED (≥0.67) = drug-like; Medium (0.34–0.67) = borderline; Low (<0.34) = non-drug-like. Use after DrugProps_lipinski_filter for a more nuanced drug...
DrugProps lipinski filter
Check drug-likeness of a compound using Lipinski Rule of Five (Ro5), Veber, Pfizer 3/75, Egan, and Ghose filters. Returns MW, cLogP, HBD, HBA, TPSA, RotBonds, Csp3 fraction, and pass/fail status for each filter. Essential first step in hit-to-lead optimization. Lipinski Ro5 (pass = drug-like): MW≤500, cLogP≤5, HBD≤5, HBA≤10 (max 1 violation). Veber (oral bioavailability): RotBonds≤10, TPSA≤140. Pfizer 3/75 (reduces promiscuity): cLogP≤3, TPSA≥75. Examples: aspirin ('CC(=O)Oc1ccccc1C(=O)O') pa...
DrugProps pains filter
Screen a compound for PAINS (Pan-Assay Interference Compounds), Brenk undesirable substructures, and NIH alerts using RDKit FilterCatalog. PAINS compounds produce false positives in biochemical assays due to non-specific activity mechanisms (rhodanines, quinones, catechols, etc.). Brenk filter flags reactive/toxic groups (Michael acceptors, epoxides, nitroaromatics, etc.). Returns match details and remediation recommendations. Essential quality filter before committing to high-throughput scre...
DrugSynergy calculate bliss
Calculate Bliss Independence synergy score for a drug combination. Model: E_expected = E_a + E_b - E_a*E_b. Synergy score = (E_combo - E_expected) * 100. Positive = synergy; Negative = antagonism. Inputs are fractional inhibition values (0-1). Based on Bliss (1939). Use for: single-concentration combination screening, high-throughput synergy assessment.
DrugSynergy calculate ci
Calculate Chou-Talalay Combination Index (CI) for drug synergy quantification. CI is derived from the Median Effect Equation: fa/fu = (D/Dm)^m. CI < 1 indicates synergy, CI = 1 is additive, CI > 1 is antagonism. Also computes the Dose Reduction Index (DRI) showing how much each drug dose can be reduced in combination. Supports both mutually exclusive (drugs with similar mechanisms) and mutually non-exclusive (drugs with different mechanisms) assumptions. Based on Chou & Talalay (1984). Use fo...
DrugSynergy calculate loewe
Calculate Loewe Additivity synergy score for a drug combination. The Loewe model is the most widely used reference model for drug interaction: d_a/D_a(E) + d_b/D_b(E) = 1 at additivity. If sum < 1, the combination is synergistic (needs less drug than expected); if > 1, it is antagonistic. Requires single-agent dose-response data for each drug (to fit Hill curves) plus the combination doses and observed effect. Based on Loewe & Muischnek (1926). Use for: rigorous synergy quantification with do...
DrugSynergy calculate zip
Calculate ZIP (Zero Interaction Potency) delta synergy score from a full dose-response matrix. Fits Hill curves to marginal dose-response data for each drug and calculates expected additivity. Returns delta matrix where positive values indicate synergy. Based on Yadav et al. (2015). IMPORTANT: Each drug must have ≥3 non-zero dose points with measurable inhibition for Hill curve fitting to succeed. A 3×3 matrix with non-zero doses_a and doses_b (no zero-dose rows/columns) is the minimum; 4×4 o...
DrugSynergy calculate hsa
Calculate Highest Single Agent (HSA) synergy score for drug combinations across dose points. HSA expected = max(E_a, E_b) at each dose. Synergy = observed - HSA expected. Requires matching arrays of effects for drug A, drug B, and the combination. Use for: multi-dose combination matrices, identifying synergistic dose ranges.
EnsemblPheno get by gene
Get phenotype associations for a gene from the Ensembl REST API. Returns diseases, traits, and clinical conditions linked to the gene, aggregated from multiple sources including Cancer Gene Census, OMIM, ClinVar, NHGRI-EBI GWAS catalog, and Orphanet. Each entry includes the phenotype description, data source, genomic location, and ontology accessions (EFO, HP, Orphanet). Example: BRCA1 returns 162 phenotype associations across multiple cancer types and other conditions.
EnsemblPheno get by region
Get phenotype associations for all variants and genes in a genomic region from the Ensembl REST API. Returns disease/trait associations from GWAS catalog, ClinVar, Cancer Gene Census, etc. for features overlapping the specified region. Useful for understanding the phenotypic landscape of a genomic interval, especially for interpreting GWAS loci or candidate regions. Example: TP53 region (chr17:7661779-7687538) returns phenotype associations from the NHGRI-EBI GWAS catalog.
EnsemblPheno get by variant
Get phenotype associations for a specific variant (by rsID) from the Ensembl REST API. Returns traits, diseases, and phenotypes associated with the variant from NHGRI-EBI GWAS catalog, ClinVar, and other sources. Includes risk alleles, beta coefficients/odds ratios, p-values, and study references. Example: rs429358 (APOE epsilon 4 variant) returns 1004 phenotype associations including Alzheimer disease, LDL cholesterol levels, and metabolite measurements.
EnsemblVEP annotate hgvs
Predict functional consequences of a genetic variant using HGVS notation via the Ensembl Variant Effect Predictor (VEP). Returns impact on genes, transcripts, and proteins including SIFT/PolyPhen pathogenicity scores, consequence types, amino acid changes, and colocated known variants. HGVS notation examples: 'BRAF:p.Val600Glu' (protein), 'ENST00000366667:c.803C>T' (coding DNA). This complements the existing region-based VEP tool by accepting standard clinical variant nomenclature.
EnsemblVEP annotate rsid
Predict functional consequences of a genetic variant using its dbSNP rs identifier via the Ensembl Variant Effect Predictor (VEP). Returns impact on genes, transcripts, and proteins including SIFT/PolyPhen scores, consequence types, amino acid changes, and colocated variants. Useful when you have a variant's rs number from GWAS, clinical reports, or literature. Example: 'rs7903146' (TCF7L2 T2D variant), 'rs429358' (APOE Alzheimer variant).
EnsemblVEP variant recoder
Convert genetic variant identifiers between different nomenclature formats using the Ensembl Variant Recoder. Given a variant ID (e.g., rs number), returns equivalent representations in HGVS genomic (hgvsg), HGVS coding (hgvsc), HGVS protein (hgvsp), and SPDI format. Essential for cross-referencing variants across databases that use different notation systems. Example: 'rs429358' returns HGVS coding notation for all APOE transcripts.
EuropePMC get citations
Get citations for an article from Europe PMC. Citations are articles that cite the specified article. Requires a source (e.g., 'MED' for PubMed, 'PMC' for PMC) and article ID. Use EuropePMC_search_articles to find article IDs first.
EuropePMC get fulltext snippets
Fetch an article's full text (best-effort) and return bounded text snippets around provided terms. Uses deterministic fallbacks: Europe PMC fullTextXML → NCBI PMC OAI (JATS) → NCBI efetch (XML) → PMC HTML. Returns a machine-readable retrieval_trace so callers can see exactly what succeeded/failed.
EuropePMC get fulltext
Fetch a PMC article's full text with deterministic fallbacks: Europe PMC fullTextXML → NCBI PMC OAI (JATS) → NCBI efetch (XML) → PMC HTML. Designed for machine consumption: returns structured provenance (source/format/content_type) and a retrieval_trace of every attempt.
EuropePMC get references
Get references (bibliography) for an article from Europe PMC. References are articles cited by the specified article. Requires a source (e.g., 'MED' for PubMed, 'PMC' for PMC) and article ID. Use EuropePMC_search_articles to find article IDs first.
EuropePMC Guidelines Search
Search Europe PMC for clinical guidelines and evidence-based recommendations. Europe PMC provides free access to a comprehensive archive of life sciences literature, including clinical practice guidelines from international sources.
EuropePMC search articles
Search for articles on Europe PMC including abstracts and metadata. Europe PMC supports fielded queries for indexed full text (e.g., BODY:"term") but only for records where Europe PMC has full text indexed (HAS_FT:Y). Use require_has_ft/fulltext_terms to avoid confusing 'has a full-text link somewhere' with 'full text searchable in Europe PMC'.
europepmc disease target score
Extract disease-target association scores from Europe PMC literature. This includes literature-based evidence.
eva disease target score
Extract disease-target association scores from EVA (European Variation Archive). EVA provides genetic variant data.
eva somatic disease target score
Extract disease-target association scores from EVA somatic mutations. This includes somatic variant data.
expression atlas disease target score
Extract disease-target association scores from Expression Atlas. This provides gene expression data.
extract clinical trial adverse events
Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.
extract clinical trial outcomes
Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clinicaltrials.gov, using their NCT IDs.
FAERS calculate disproportionality
Calculate statistical disproportionality measures (ROR, PRR, IC) with 95% CI for drug-event pairs. Returns signal strength classification. Example: drug='ibuprofen', event='hepatotoxicity' → ROR=2.3 [1.8-2.9]. Use for pharmacovigilance signal detection.
FAERS analyze temporal trends
Analyze temporal trends in adverse event reporting by year. Returns yearly counts and trend direction (increasing/decreasing/stable). Example: ibuprofen GI bleeding reports 2015-2025 → +25% increase. Use for signal evolution monitoring.
FAERS compare drugs
Compare safety signals for two drugs with the same adverse event. Returns ROR/PRR/IC for both drugs with comparative analysis. Example: compare fulvestrant vs tamoxifen for hepatotoxicity. Use for safety benchmarking.
FAERS count additive administration routes
Enumerate and count administration routes for adverse events across specified medicinal products. Only medicinalproducts is required; serious filter is optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count additive adverse reactions
Aggregate adverse reaction counts across specified medicinal products. Only medicinalproducts is required; all other filters (patientsex, patientagegroup, occurcountry, serious, seriousnessdeath) are optional. Use filters sparingly to avoid overly restrictive searches that return no results. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count additive event reports by country
Aggregate report counts by country of occurrence across specified medicinal products. Only medicinalproducts is required; all other filters (patientsex, patientagegroup, serious) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count additive reaction outcomes
Determine reaction outcome counts (e.g., recovered, resolving, fatal) across medicinal products. Only medicinalproducts is required; all other filters (patientsex, patientagegroup, occurcountry) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count additive reports by reporter country
Aggregate adverse event reports by primary reporter country across medicinal products. Only medicinalproducts is required; all other filters (patientsex, patientagegroup, serious) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count additive seriousness classification
Quantify serious vs non-serious classifications across medicinal products. Only medicinalproducts is required; all other filters (patientsex, patientagegroup, occurcountry) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count country by drug event
Count the number of adverse event reports per country of occurrence. Only medicinalproduct is required; all other filters (patientsex, patientagegroup, serious) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count death related by drug
Count adverse events associated with patient death for a given drug. Only medicinalproduct is required. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count drug routes by event
Count the most common routes of administration for drugs involved in adverse event reports. Only medicinalproduct is required; serious filter is optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count drugs by drug event
Count the number of different drugs involved in FDA adverse event reports. All filters (patientsex, patientagegroup, occurcountry, serious) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count outcomes by drug event
Count the outcome of adverse reactions (recovered, recovering, fatal, unresolved). Only medicinalproduct is required; all other filters (patientsex, patientagegroup, occurcountry) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count patient age distribution
Analyze the age distribution of patients experiencing adverse events for a specific drug. Only medicinalproduct is required. The age groups are: Neonate (0-28 days), Infant (29 days - 23 months), Child (2-11 years), Adolescent (12-17 years), Adult (18-64 years), Elderly (65+ years). Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count reactions by drug event
Count the number of adverse reactions reported for a given drug. Only medicinalproduct is required; all other filters (patientsex, patientagegroup, occurcountry, serious, seriousnessdeath, reactionmeddraverse) are optional. When reactionmeddraverse is not specified, returns all adverse reactions (AE) with their counts grouped by MedDRA Preferred Term. When reactionmeddraverse is specified, filters results to only include that specific MedDRA Lowest Level Term. Use filters sparingly to avoid o...
FAERS count reportercountry by drug event
Count the number of FDA adverse event reports grouped by the country of the primary reporter. Only medicinalproduct is required; all other filters (patientsex, patientagegroup, serious) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS count seriousness by drug event
Count the number of adverse event reports classified as serious or non-serious. Only medicinalproduct is required; all other filters (patientsex, patientagegroup, occurcountry) are optional. Use filters sparingly to avoid overly restrictive searches. In results, term Serious means: "The adverse event resulted in death, a life threatening condition, hospitalization, disability, congenital anomaly, or other serious condition", term Non-serious means "The adverse event did not result in any o...
FAERS filter serious events
Filter for serious adverse events (death, hospitalization, disability, life-threatening). Returns top reactions meeting seriousness criteria. Example: fulvestrant serious events → Death: 150 cases, Hospitalization: 500 cases. Use for risk-benefit assessment.
FAERS rollup meddra hierarchy
Aggregate adverse events by MedDRA hierarchy (Preferred Term level). Returns top 50 PTs with counts. Note: Full HLT/SOC hierarchy requires MedDRA license. Use for adverse event profile overview.
FAERS search adverse event reports
Search and retrieve detailed adverse event reports from FAERS. Returns individual case reports with patient information, adverse event details, drug information, and report metadata. Only medicinalproduct is required; all other parameters (limit, skip, patientsex, patientagegroup, occurcountry, serious, seriousnessdeath) are optional. Use filters sparingly to avoid overly restrictive searches. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS search reports by drug and outcome
Search and retrieve detailed adverse event reports for a specific drug filtered by reaction outcome. Returns individual case reports with patient information, adverse event details, drug information, and report metadata. Only medicinalproduct is required; all other parameters (reactionoutcome, limit, skip, patientsex, patientagegroup, serious) are optional. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS search reports by drug and indication
Search and retrieve detailed adverse event reports for a specific drug and indication. Returns individual case reports with patient information, adverse event details, drug information, and report metadata. Only medicinalproduct is required; all other parameters (drugindication, limit, skip, patientsex, patientagegroup, serious) are optional. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS search reports by drug combination
Search and retrieve detailed adverse event reports involving multiple drugs (drug interactions). Returns individual case reports where all specified drugs are present. Only medicinalproducts (list of at least 2 drug names) is required; all other parameters (limit, skip, patientsex, patientagegroup, serious) are optional. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS search reports by drug and reaction
Search and retrieve detailed adverse event reports for a specific drug and reaction type. Returns individual case reports with patient information, adverse event details, drug information, and report metadata. Only medicinalproduct and reactionmeddrapt are required; all other parameters (limit, skip, patientsex, patientagegroup, serious) are optional. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS search serious reports by drug
Search and retrieve detailed reports of serious adverse events for a specific drug. Returns individual case reports with patient information, adverse event details, drug information, and report metadata. Only medicinalproduct is required; all other parameters (limit, skip, seriousnessdeath, seriousnesshospitalization, seriousnesslifethreatening, seriousnessdisabling, patientsex, patientagegroup) are optional. Data source: FDA Adverse Event Reporting System (FAERS).
FAERS stratify by demographics
Stratify adverse event reports by demographics (sex, age group, country). Returns counts and percentages by demographic group. Example: ibuprofen + GI bleeding stratified by sex → Female: 60%, Male: 40%. Use for subpopulation risk assessment.
FDA get abuse dependence info by drug name
Get information about drug abuse and dependence based on the drug name, specifically information on whether the drug is a controlled substances, the types of possible abuse, and adverse reactions relevant to those abuse types.
FDA get abuse info by drug name
Retrieve information about types of abuse based on the drug name.
FDA get accessories info by drug name
Retrieve information about accessories based on the drug name.
FDA get active ingredient info by drug name
Fetch a list of active ingredients in a specific drug product.
FDA get adverse reactions by drug name
Retrieve adverse reactions information based on the drug name.
FDA get alarms by drug name
Retrieve alarms based on the specified drug name.
FDA get animal pharmacology info by drug name
Retrieve animal pharmacology and toxicology information based on drug names.
FDA get assembly installation info by drug name
Retrieve assembly or installation instructions based on drug names.
FDA get boxed warning info by drug name
Retrieve boxed warning and adverse effects information for a specific drug.
FDA get brand name generic name
Retrieve the brand name and generic name from generic name or brand name of a drug.
FDA get carcinogenic mutagenic fertility by drug name
Retrieve carcinogenic, mutagenic, or fertility impairment information based on the drug name.
FDA get child safety info by drug name
Retrieve child safety information for a specific drug based on its name.
FDA get clinical pharmacology by drug name
Retrieve clinical pharmacology information based on drug names.
FDA get clinical studies info by drug name
Retrieve clinical studies information based on the drug name.
FDA get consulting doctor pharmacist info by drug name
Get information about when a doctor or pharmacist should be consulted regarding drug interactions for a specific drug.
FDA get conditions info for doctor consult by drug name
Get information about when a doctor should be consulted before using a specific drug.
FDA get contraindications by drug name
Retrieve contraindications information based on the drug name.
FDA get contact for questions info by drug name
Retrieve information on who to contact with questions about the drug based on the provided drug name.
FDA get DEA schedule info by drug name
Retrieve information about the controlled substance Drug Enforcement Administratino (DEA) schedule for a specific drug.
FDA get dependence info by drug name
Retrieve information about dependence characteristics based on the drug name.
FDA get dhcp letter info by drug name
Fetch information about dear health care provider letters for a specific drug. The letters are sent by drug manufacturers to provide new or updated information about the drug.
FDA get disposal info by drug name
Retrieve disposal and waste handling information based on the drug name.
FDA get do not use info by drug name
Retrieve information about all contraindications for use based on the drug name.
FDA get document id by drug name
Retrieve the document ID based on the drug name.
FDA get dosage and storage information by drug name
Retrieve dosage and storage information for a specific drug.
FDA get drug generic name
Get the drug’s generic name based on the drug's generic or brand name.
FDA get dosage forms and strengths by drug name
Retrieve dosage forms and strengths information based on the drug name.
FDA get drug interactions by drug name
Retrieve drug interactions based on the specified drug name.
FDA get drug label info by field value
Retrieve FDA drug label information by searching a specific FDA drug label field for a given value (field:value). This is a generic field-based lookup. Use `return_fields` to choose which sections/fields to return, or pass "ALL" to return full label records. Note: for `openfda.generic_name`, values are typically uppercase (e.g., "ASPIRIN"). Allowed fields (use these for both `field` and `return_fields`): abuse, accessories, active_ingredient, adverse_reactions, alarms, animal_pharmacolog...
FDA get drug label
Get the complete FDA-approved prescribing information for a specific drug by name. Returns all clinical sections of the official drug label: indications, dosing regimens, contraindications, black box warnings, drug interactions, use in specific populations (pregnancy, pediatrics, renal/hepatic impairment), pharmacokinetics, mechanism of action, and adverse reactions. This is the authoritative source for FDA-approved drug clinical information in the US.
FDA get drug name by adverse reaction
Retrieve the drug name based on specific adverse reactions reported. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug name by conditions for doctor consult
Retrieve the drug names that require asking a doctor before use due to a patient's specific conditions and symptoms. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug name by dependence info
Retrieve the drug name based on information about dependence characteristics.
FDA get drug name by document id
Retrieve the drug name based on the document ID.
FDA get drug name by dosage info
Retrieve the drug name based on dosage and administration information.
FDA get drug name by environmental warning
Retrieve the drug name based on the specified environmental warnings.
FDA get drug name by inactive ingredient
Retrieve the drug name based on the inactive ingredient information.
FDA get drug name by labor and delivery info
Retrieve the drug name based on information about the drug’s use during labor or delivery.
FDA get drug name by microbiology
Retrieve the drug name based on microbiology field information.
FDA get drug name by other safety info
Retrieve the drug name based on the provided safety information. This tool looks through safety information that may not be specified in other fields.
FDA get drug name by pharmacodynamics
Retrieve the drug name based on pharmacodynamics information.
FDA get drug name by pharmacogenomics
Retrieve the drug name based on pharmacogenomics field information.
FDA get drug name by precautions
Retrieve the drug name based on the precautions field information.
FDA get drug name by pregnancy or breastfeeding info
Retrieve the drug names based on pregnancy or breastfeeding information.
FDA get drug name by principal display panel
Retrieve the drug name based on the content of the principal display panel of the product package.
FDA get drug name by reference
Retrieve the drug name based on the reference information provided in the drug labeling.
FDA get drug name by set id
Retrieve the drug name based on the Set ID of the labeling.
FDA get drug name by SPL ID
Retrieve the drug name based on the FDA application number, NUI unique identifier, document ID of a specific version of the drug's Structured Product Label (SPL), or set ID of the drug's Structured Product Label that works across label versions.
FDA get drug name by stop use info
Retrieve the drug name based on the stop use information provided.
FDA get drug name by storage and handling info
Retrieve the drug name based on storage and handling information.
FDA get drug name by warnings
Retrieve the drug names based on specific warning information.
FDA get drug name from patient package insert
Retrieve the drug name based on the information provided in the patient package insert.
FDA get drug names by abuse dependence info
Retrieve the drug name based on information about drug abuse and dependence, including whether the drug is a controlled substances, the types of possible abuse, and adverse reactions relevant to those abuse types.
FDA get drug names by abuse info
Retrieve drug names based on information about types of abuse and adverse reactions pertinent to those types of abuse. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by accessories
Retrieve drug names based on the accessories field information.
FDA get drug names by active ingredient
Retrieve drug names based on the active ingredient information.
FDA get drug names by alarm
Retrieve drug names based on the presence of specific alarms, which are related to adverse reaction events. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by animal pharmacology info
Retrieve drug names based on animal pharmacology and toxicology information. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by application number NDC number
Retrieve drug names based on the specified FDA application number or National Drug Code (NDC) number.
FDA get drug names by assembly installation info
Retrieve drug names based on assembly or installation instructions. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by boxed warning
Retrieve drug names that have specific boxed warnings and adverse effects.
FDA get drug names by child safety info
Retrieve drug names based on whether the product should be kept out of the reach of children and instructions about what to do in the case of accidental contact or ingestion.
FDA get drug names by clinical pharmacology
Retrieve drug names based on clinical pharmacology information. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by clinical studies
Retrieve drug names based on the presence of clinical studies information.
FDA get drug names by contraindications
Retrieve drug names based on specific contraindications information.
FDA get drug names by consulting doctor pharmacist info
Retrieve drug names based on information about when a doctor or pharmacist should be consulted regarding drug interactions. Warning: This tool only outputs a predefined limited number of drug names and does not cover all possible drugs. Use with caution.
FDA get drug names by controlled substance DEA schedule
Retrieve drug names based on the Drug Enforcement Administration (DEA) schedule information.
FDA get drug names by dhcp letter info
Fetch drug names based on information about dear health care provider letters. The letters are sent by drug manufacturers to provide new or updated information about the drug.
FDA get drug names by disposal info
Retrieve drug names based on disposal and waste handling information.
FDA get drug names by dosage forms and strengths info
Retrieve drug names based on specific dosage forms and strengths information.
FDA get drug names by drug interactions
Retrieve a list of drug names that have the specified drug interactions.
FDA get drug names by effective time
Retrieve drug names based on the effective time of the labeling document.
FDA get drug names by food safety warnings
Retrieve drug names based on specific food safety warnings.
FDA get drug names by general precautions
Retrieve drug names based on specific general precautions information.
FDA get drug names by geriatric use
Retrieve drug names that have specific information about geriatric use.
FDA get drug names by health claim
Retrieve drug names based on specific health claims.
FDA get drug names by indication aggregated
Retrieve and aggregate drug names by indication, grouping by generic name with all brand names. This tool iterates through all available results without limit restrictions.
FDA get drug names by indication stats
Retrieve and aggregate drug names by indication using FDA count API. This tool uses count mechanism to efficiently get brand_name and generic_name distributions without fetching full records.
FDA get drug names by indication
Retrieve a list of drug names based on a specific indication or usage.
FDA get drug names by info for nursing mothers
Retrieve drug names based on information related to nursing mothers.
FDA get drug names by info for owner or caregiver
Retrieve drug names based on information for owners or caregivers.
FDA get drug names by ingredient
Retrieve drug names based on a specific ingredient present in the drug product.
FDA get drug names by lab test interference
Retrieve drug names that have known interference with laboratory tests.
FDA get drug names by instructions for use
Retrieve drug names based on specific instructions for use.
FDA get drug names by lab tests
Retrieve drug names based on laboratory tests information.
FDA get drug names by medication guide
Retrieve drug names based on the presence of specific information in the medication guide.
FDA get drug names by mechanism of action
Retrieve drug names based on the specified mechanism of action information.
FDA get drug names by nonclinical toxicology info
Retrieve drug names based on nonclinical toxicology information.
FDA get drug names by nonteratogenic effects
Retrieve drug names based on the presence of nonteratogenic effects information.
FDA get drug names by overdosage info
Retrieve drug names based on information about signs, symptoms, and laboratory findings of acute overdosage.
FDA get drug names by pharmacokinetics
Retrieve drug names based on specific pharmacokinetics information, such as absorption, distribution, elimination, metabolism, drug interactions, and specific patient populations.
FDA get drug names by pediatric use
Retrieve drug names based on pediatric use information.
FDA get drug names by population use
Retrieve drug names based on their use in specific populations, such as pregnant women, nursing mothers, pediatric patients, and geriatric patients.
FDA get drug names by pregnancy effects info
Retrieve drug names based on information about effects the drug may have on pregnant women or on a fetus.
FDA get drug names by residue warning
Retrieve drug names based on the presence of residue warnings.
FDA get drug names by risk
Retrieve drug names based on specific risk information, especially regarding pregnancy or breastfeeding.
FDA get drug names by safe handling warning
Retrieve drug names that have specific safe handling warnings.
FDA get drug names by route
Retrieve the drug names based on the route of administration.
FDA get drug names by safety summary
Retrieve drug names based on the summary of safety and effectiveness information.
FDA get drug names by spl indexing data elements
Retrieve drug names based on Structured Product Labeling (SPL) indexing data elements.
FDA get drug names by teratogenic effects
Retrieve drug names based on specific teratogenic effects categories.
FDA get drug names by user safety warning
Retrieve drug names that have specific user safety warnings.
FDA get drug names by warnings and cautions
Retrieve drug names based on specific warnings and cautions information.
FDA get drugs by carcinogenic mutagenic fertility
Retrieve drug names based on the presence of carcinogenic, mutagenic, or fertility impairment information.
FDA get effective time by drug name
Retrieve effective time of the labeling document based on the drug name.
FDA get environmental warning by drug name
Fetch environmental warnings for a specific drug based on its name.
FDA get general precautions by drug name
Retrieve general precautions information based on the drug name.
FDA get geriatric use info by drug name
Retrieve information about geriatric use based on the drug name.
FDA get health claims by drug name
Retrieve health claims associated with a specific drug name.
FDA get inactive ingredient info by drug name
Fetch a list of inactive ingredients in a specific drug product based on the drug name.
FDA get indications by drug name
Retrieve indications and usage information based on a specific drug name.
FDA get info for nursing mothers by drug name
Retrieve information about nursing mothers for a specific drug.
FDA get info for owner caregiver by drug name
Retrieve specific information for owners or caregivers based on the drug name.
FDA get info for patients by drug name
Fetch information for patients based on the drug name.
FDA get ingredients by drug name
Retrieve a list of drug ingredients based on the drug name.
FDA get instructions for use by drug name
Retrieve instructions for use information based on the drug name.
FDA get lab test interference info by drug name
Retrieve information about laboratory test interferences for a specific drug.
FDA get lab tests by drug name
Retrieve laboratory tests information based on drug names.
FDA get labor and delivery info by drug name
Retrieve information about the drug’s use during labor or delivery based on the drug name.
FDA get manufacturer name NDC number by drug name
Retrieve detailed information about a drug's active ingredient, FDA application number, manufacturer name, National Drug Code (NDC) number, and route of administration; all based on the drug name.
FDA get medication guide info by drug name
Retrieve medication guide information based on the drug name.
FDA get microbiology info by drug name
Retrieve microbiology information based on the drug name.
FDA get nonclinical toxicology info by drug name
Retrieve nonclinical toxicology information based on drug names.
FDA get mechanism of action by drug name
Retrieve the mechanism of action information for a specific drug.
FDA get nonteratogenic effects by drug name
Retrieve information about nonteratogenic effects based on the drug name.
FDA get other safety info by drug name
Retrieve safety information that may not be specified in other fields based on the provided drug name.
FDA get overdosage info by drug name
Retrieve information about signs, symptoms, and laboratory findings of acute overdosage based on the drug name.
FDA get patient package insert from drug name
Retrieve the patient package insert information based on the drug name.
FDA get pediatric use info by drug name
Retrieve pediatric use information based on drug names.
FDA get pharmacodynamics by drug name
Retrieve pharmacodynamics information based on the drug name.
FDA get pharmacogenomics info by drug name
Retrieve pharmacogenomics information based on the drug name.
FDA get pharmacokinetics by drug name
Retrieve pharmacokinetics information (e.g. absorption, distribution, elimination, metabolism, drug interactions, and specific patient populations) for a specific drug based on its name.
FDA get population use info by drug name
Retrieve information about the use of a drug in specific populations based on the drug name.
FDA get precautions by drug name
Retrieve precautions information based on the drug name.
FDA get pregnancy effects info by drug name
Retrieve information about the effects on pregnancy for a specific drug.
FDA get pregnancy or breastfeeding info by drug name
Retrieve the pregnancy or breastfeeding information based on the specified drug name.
FDA get principal display panel by drug name
Retrieve the content of the principal display panel of the product package based on the drug name.
FDA get purpose info by drug name
Retrieve about the drug product’s indications for use based on the drug name.
FDA get recent changes by drug name
Retrieve recent major changes in labeling for a specific drug.
FDA get reference info by drug name
Retrieve reference information based on the drug name provided.
FDA get risk info by drug name
Retrieve risk information (especially regarding pregnancy or breastfeeding) based on the drug name.
FDA get route info by drug name
Retrieve the route of administration information based on the drug name.
FDA get safe handling warnings by drug name
Retrieve safe handling warnings for a specific drug based on its name.
FDA get safety summary by drug name
Retrieve a summary of safety and effectiveness information based on the drug name.
FDA get spl indexing data elements by drug name
Retrieve Structured Product Labeling (SPL) indexing data elements based on drug names.
FDA get spl unclassified section by drug name
Retrieve the SPL unclassified section information based on the drug name.
FDA get storage and handling info by drug name
Retrieve storage and handling information based on the drug name.
FDA get stop use info by drug name
Retrieve stop use information based on the drug name provided.
FDA get teratogenic effects by drug name
Retrieve teratogenic effects information based on the drug name.
FDA get user safety warning by drug names
Retrieve specific user safety warnings based on drug names.
FDA get warnings and cautions by drug name
Retrieve warnings and cautions information for a specific drug based on its name.
FDA get warnings by drug name
Retrieve warning information based on the drug name.
FDA get when using info
Retrieve information about side effects and substances or activities to avoid while using a specific drug.
FDA list drug classes
List FDA pharmacological drug classes (Established Pharmacologic Class, EPC) and the number of drug products in each class. Classes include designations like 'Selective Serotonin Reuptake Inhibitor [EPC]', 'Beta-Adrenergic Blocker [EPC]', 'HMG-CoA Reductase Inhibitor [EPC]' (statins), 'ACE Inhibitor [EPC]', etc. Use this to discover drug class names for filtering or understanding drug categorization.
FDA OrangeBook check generic availability
Check if generic versions are FDA-approved for a brand-name drug. Returns reference drug info, approved generics count, and TE codes. Example: Query 'LIPITOR' to find atorvastatin generics. Use for competitive landscape analysis.
FDA OrangeBook get approval history
Get complete approval history for a drug application including original approval date, supplements, and review documents. Returns submission timeline and links to approval letters/labels. Example: NDA020402 shows all Advil approval actions.
FDA OrangeBook get patent info
Get patent information for approved drugs. Note: Full patent details (numbers, expiration dates) require Orange Book data files download. Returns guidance on accessing complete patent data. Use for regulatory exclusivity planning.
FDA OrangeBook get exclusivity
Get drug exclusivity information (NCE, orphan, pediatric). Note: Specific expiration dates require Orange Book data files. Returns exclusivity types (5-year NCE, 3-year clinical study, 7-year orphan, 180-day generic). Use for generic launch planning.
FDA OrangeBook get te code
Get therapeutic equivalence (TE) codes for drug products. AB=bioequivalent/substitutable, AT=topical equivalent, B*=NOT therapeutically equivalent. Returns TE codes with interpretation guide. Use for generic substitution decisions.
FDA OrangeBook search drug
Search FDA Drugs@FDA database by brand name, generic name, or application number. Returns approval status, products, and basic regulatory info. Example: brand_name='ADVIL' finds all Advil products with NDA numbers.
fda pharmacogenomic biomarkers
Retrieve pharmacogenomic biomarkers from FDA drug labels. This tool fetches the Table of Pharmacogenomic Biomarkers in Drug Labeling from the FDA website and allows filtering by drug name or biomarker.
FDA retrieve device use by drug name
Retrieve the intended use of the device based on the drug name.
FDA retrieve drug name by device use
Retrieve the drug name based on the intended use of the device.
FDA retrieve drug names by patient medication info
Retrieve drug names based on patient medication information, which is about safe use of the drug.
FDA retrieve patient medication info by drug name
Retrieve patient medication information (which is about safe use of the drug) based on drug names.
FDA search drug labels
Search FDA-approved drug labels (prescribing information) by drug name or medical indication. Drug labels contain official clinical guidance: indications, dosing regimens, contraindications, black box warnings, drug interactions, and adverse reactions. Use drug_name for drug-specific lookups (e.g., 'metformin', 'warfarin') or indication for condition-based searches (e.g., 'hypertension', 'type 2 diabetes'). Returns a list of matching drug labels with key clinical sections.
G2P get gene
Get Gene2Phenotype information for a specific gene by symbol. Returns gene location, cross-references to HGNC/Ensembl/OMIM, gene synonyms, and genomic coordinates. This provides the gene-level data without disease associations. For disease associations, use G2P_search with the gene name instead.
G2P get panel
Get summary statistics for a Gene2Phenotype clinical panel. G2P organizes gene-disease associations into expert-curated panels: DD (developmental disorders), Cancer, Skeletal, Eye, Cardiac, Ear, Skin, and Prenatal. Returns panel name, description, last update date, total records count, total genes, and breakdown by confidence level (definitive, strong, moderate, limited).
G2P get record
Get detailed Gene2Phenotype (G2P) record for a specific gene-disease association by its stable ID. Returns comprehensive clinical genetics information including locus details (gene symbol, genomic coordinates, cross-references), genotype/inheritance pattern, variant consequences (with Sequence Ontology terms), molecular mechanism with evidence, disease details with ontology terms, confidence level, and supporting publications. Use G2P_search first to find stable IDs.
G2P search
Search the Gene2Phenotype (G2P) database for gene-disease associations curated by clinical geneticists. G2P is maintained by EBI and provides expert-curated evidence for gene-disease relationships used in clinical diagnosis. Returns gene-disease pairs with genotype (monoallelic/biallelic), molecular mechanism (loss/gain of function), clinical panel assignment (DD, Cancer, Skeletal, etc.), and confidence level (definitive, strong, moderate, limited). Useful for clinical variant interpretation ...
GDC get cnv data
Query copy number variation (CNV) files from GDC/TCGA projects. Returns CNV segment and gene-level copy number files. Use for amplification/deletion analysis.
GDC get gene expression
Query RNA-Seq gene expression files from GDC/TCGA projects. Returns file metadata for expression quantification data. Use to find expression data for downstream analysis.
GDC get mutation frequency
Get mutation frequency statistics for a gene across all TCGA/GDC cancer projects. Returns total SSM occurrence count and per-project case counts via /ssm_occurrences faceting. Also returns gene metadata (biotype, cancer gene census status). Answers 'How often is this gene mutated across cancers?'
GDC get ssm by gene
Get somatic mutations (SSMs) for a gene across TCGA/GDC projects. Returns mutation type, genomic coordinates, and amino acid changes. Essential for pan-cancer mutation analysis.
GDC list files
List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e.g., expression quantification) for analysis pipelines.
GDC list projects
List GDC projects (TCGA, TARGET, etc.) with case/file counts. Use to discover available cancer cohorts and their data volume. Filter by program (TCGA, TARGET, CGCI, etc.).
GDC search cases
Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata for cohort construction and downstream file queries.
GenomeNexus annotate mutation
Annotate a cancer mutation using Genome Nexus (MSK) by specifying chromosome, start, end, reference allele, and variant allele separately. This is an alternative to the HGVS-based annotation for when you have genomic coordinates directly (GRCh37/hg19). Returns the same comprehensive annotation as GenomeNexus_annotate_variant including VEP consequences, SIFT, PolyPhen, AlphaMissense scores, cancer hotspots, and mutation assessor. Example: chr=7, start=140453136, end=140453136, ref=A, alt=T for...
GenomeNexus annotate variant
Annotate a genomic variant using Genome Nexus (Memorial Sloan Kettering), which aggregates variant annotations from multiple sources including VEP, SIFT, PolyPhen-2, AlphaMissense, cancer hotspots, and mutation assessor. Input is a GRCh37/hg19 HGVS genomic notation (e.g., '7:g.140453136A>T' for BRAF V600E, '17:g.7577120C>T' for TP53 R273H). Returns the most severe consequence, transcript consequences with pathogenicity scores (SIFT, PolyPhen, AlphaMissense), cancer hotspot information, and an...
GenomeNexus get cancer hotspots
Get cancer mutation hotspot annotations from Genome Nexus (MSK) for a specific genomic variant. Cancer hotspots are recurrently mutated residues in cancer, curated by the Chang et al. study. Returns hotspot residue, tumor count, hotspot type (single residue or 3D cluster), and the gene symbol. Use this to check if a variant falls in a known cancer hotspot. Input is a GRCh37/hg19 HGVS genomic variant. Example: '7:g.140453136A>T' (BRAF V600E) returns V600 hotspot with 897 tumors.
GenomeNexus get canonical transcript
Get the canonical transcript for a gene from Genome Nexus (MSK). Returns the Ensembl transcript ID, protein ID, protein length, RefSeq mRNA ID, CCDS ID, HUGO symbol, and Pfam protein domain annotations. Useful for determining the standard transcript to use for variant annotation, and for getting a quick overview of protein domain architecture. Input is a HUGO gene symbol (e.g., 'TP53', 'BRAF', 'BRCA1').
genomics england disease target score
Extract disease-target association scores from Genomics England data. This includes clinical genomics evidence.
get clinical trial conditions and interventions
Retrieves the list of conditions or diseases and the interventions and arm groups that the clinical trials are focused on, using their NCT IDs.
get clinical trial descriptions
Retrieves detailed identification information for trials, including titles, phases, and descriptions, using their NCT IDs.
get clinical trial locations
Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.
get clinical trial outcome measures
Retrieves the outcome measures for the clinical trials, using their NCT IDs.
get clinical trial references
Retrieves the references (if any) for the clinical trials, using their NCT IDs.
get clinical trial status and dates
Retrieves trial status and start and completion dates, using their NCT IDs.
get clinical trial eligibility criteria
Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.
GIN Guidelines Search
Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's largest database of clinical guidelines with over 6400 guidelines from various organizations worldwide.
gnomad get gene constraints
Get gene constraint metrics from gnomAD for a gene symbol (GRCh38). Returns constraint fields under `exac_constraint` and `gnomad_constraint` (e.g., pLI, oe_lof/oe_mis/oe_syn, exp/obs counts).
gnomad get gene
Get basic gene metadata from gnomAD by `gene_symbol` or `gene_id` (Ensembl gene ID). Use `gnomad_search_genes` to discover `gene_id`. Use the returned `canonical_transcript_id` with `gnomad_get_transcript`.
gnomad get region
Get basic regional information from gnomAD by genomic interval. Returns genes overlapping the region and a list of `variant_id` values in the region for the selected dataset. Use those IDs with `gnomad_get_variant`. Keep regions small to avoid large payloads.
gnomad get sv by gene
Get structural variants (SVs) from gnomAD v4 for a gene. Returns deletions, duplications, inversions, translocations, and complex SVs with population allele frequencies, SV type, consequence, and homozygote counts. Essential for interpreting CNVs in clinical genomics.
gnomad get sv detail
Get detailed information for a specific gnomAD structural variant by its ID (e.g., DEL_chr17_24e4872b). Returns SV coordinates, type, length, population allele frequency, consequence, and filter status. Use gnomad_get_sv_by_gene or gnomad_get_sv_by_region to discover variant IDs first.
gnomad get sv by region
Get structural variants (SVs) from gnomAD v4 overlapping a genomic region. Returns DEL/DUP/INV/BND/CPX variants with allele frequencies and consequences. Use for CNV interpretation in specific chromosomal regions. Region should be < 5Mb.
gnomad get transcript
Get basic transcript metadata from gnomAD by Ensembl transcript ID (e.g., ENST...). The response includes the linked `gene` object (gene ID + symbol). Use `gnomad_get_gene` to find a gene's `canonical_transcript_id`.
gnomad get variant
Get basic variant metadata from gnomAD by `variant_id` (format like '19-44908822-C-T'). Use `gnomad_search_variants` to discover valid `variant_id` values from an rsID query. `dataset` is required by gnomAD and defaults to `gnomad_r3`.
gnomad search genes
Search for genes in gnomAD by free-text query (typically a gene symbol). Returns matching `ensembl_id` (Ensembl gene ID) and `symbol`. Use `ensembl_id` as `gene_id` for `gnomad_get_gene`.
gnomad search variants
Search for variants in gnomAD by free-text query (commonly an rsID like 'rs7412'). Returns matching `variant_id` strings. Note: gnomAD's `variant_search` response only exposes `variant_id`. Use the returned `variant_id` with `gnomad_get_variant`.
GTEx calculate eqtl
Calculate custom eQTL for any gene-variant pair in any tissue. Dynamically calculates gene-variant association statistics including p-value, normalized effect size (NES), t-statistic, and genotype data. Works for both significant and non-significant associations. Returns detailed statistics even if association not in precomputed results. Use for: testing specific hypotheses, custom variant-gene pairs, dynamic eQTL analysis, validating findings. Requires all three: gencode_id, variant_id, and ...
GTEx get eqtl genes
Get eQTL genes (eGenes) with significant cis-eQTLs. Returns genes with at least one significant expression quantitative trait locus (eQTL) in specified tissues. Includes allelic fold change, p-values, q-values (FDR < 0.05), and effect sizes. Filter by tissue or get all eGenes. Use for: identifying genes with genetic regulation, finding tissue-specific eQTLs, studying regulatory variants, genetic association studies. Essential for understanding genetic control of gene expression.
GTEx get dataset info
Get GTEx dataset metadata and version information. Returns dataset details including GENCODE version, genome build (GRCh38/hg38), dbSNP build, sample counts, tissue counts, and release information. Shows Adult GTEx V11 details (January 2026) by default. Use for: understanding data versions, checking sample sizes, verifying genome builds, documentation. Check this first to understand what data is available.
GTEx get expression summary
Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Accepts gene symbols (TP53, BRCA1) or Ensembl IDs. Use to profile baseline expression patterns for targets/biomarkers.
GTEx get median gene expression
Get median gene expression levels across GTEx tissues. Returns median expression in TPM (Transcripts Per Million) for one or more genes across 54 tissue sites. Filter by specific tissues or get expression across all tissues. Based on Adult GTEx V11 (January 2026). Use for: tissue-specific expression profiling, identifying highly expressed genes, comparing expression patterns across tissues. Example: Get brain vs liver expression for TP53 gene.
GTEx get gene expression
Get gene expression data at individual sample level (not aggregated). Returns normalized expression values (TPM) for each sample, allowing detailed distribution analysis. Can subset by donor attributes (sex, age_bracket) for demographic-specific analysis. Much more data than median expression. Use for: expression variability analysis, outlier detection, sample-level QC, demographic comparisons. Warning: large result sets for multiple genes/tissues.
GTEx get multi tissue eqtls
Get multi-tissue eQTL meta-analysis results (Metasoft). Returns m-values (posterior probability of eQTL effect in each tissue), normalized effect sizes, p-values, and standard errors across all tissues for a gene-variant pair. Shows tissue-sharing patterns of eQTL effects. Use for: understanding tissue-specificity of eQTLs, finding shared vs tissue-specific effects, cross-tissue meta-analysis, regulatory mechanism studies. Requires gencode_id, optionally filter by variant_id.
GTEx get sample info
Get detailed GTEx sample and subject metadata. Returns sample IDs, tissue types, donor demographics (age, sex), ischemic time, RIN scores, Hardy scale, pathology notes, and QC metrics. Filter by sample ID, subject ID, tissue, demographics, or data type. Use for: sample selection, cohort design, QC filtering, demographic analysis, understanding data provenance. Essential for selecting appropriate samples for analysis.
GTEx get single tissue eqtls
Get significant single-tissue eQTL associations. Returns precomputed gene-variant associations with p-values, effect sizes (NES), and genomic positions. Query by gene ID, variant ID, tissue, or combination. Results show which genetic variants affect gene expression in specific tissues. Use for: finding eQTLs for candidate genes, looking up variant effects, tissue-specific regulatory analysis, GWAS follow-up. Must provide at least one filter: gencode_id, variant_id, or tissue_site_detail_id.
GTEx get tissue sites
Get all available GTEx tissue sites with metadata. Returns tissue IDs, names, sample counts, eGene counts, and color codes for 54 non-diseased tissue sites. Includes RNA-seq sample summaries with donor age and sex statistics. Use for: discovering available tissues, finding tissue IDs for queries, checking sample sizes, understanding tissue coverage. Essential first step before querying tissue-specific data.
GTEx get top expressed genes
Get top expressed genes in a specific tissue sorted by median expression. Returns gene list with expression levels (TPM), useful for understanding tissue-specific gene signatures. Option to filter mitochondrial genes (default: true). Use for: tissue characterization, finding housekeeping genes, identifying tissue markers, quality control. Essential for understanding what genes are active in each tissue type.
GTEx query eqtl
Query GTEx single-tissue eQTL associations for a gene. Accepts gene symbols (TP53, BRCA1) or Ensembl IDs. Use to identify regulatory variants (variantId, pValue, slope) relevant to expression regulation.
gwas get association by id
Get a specific GWAS association by its unique identifier.
gwas get associations for snp
Get all associations for a specific SNP with optional sorting.
gwas get associations for study
Get all associations for a specific study, sorted by p-value.
gwas get associations for trait
Get all associations for a specific trait, sorted by p-value (most significant first).
gwas get snp by id
Get a specific GWAS SNP by its rs ID.
gwas get snps for gene
Get all GWAS Catalog SNPs mapped to a specific gene by gene name (e.g., 'BRCA1', 'TP53'). Returns variant details including rs IDs, chromosomal positions, and functional annotations. Use this when you want to find all catalogued variants within or near a specific gene.
gwas get studies for trait
Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary statistics.
gwas get study by id
Get a specific GWAS study by its unique identifier.
gwas get variants for trait
Search the GWAS Catalog for all genetic variants (SNPs) linked to a specific disease or trait. Accepts free-text disease/trait names (e.g., 'diabetes', 'breast cancer'), EFO ontology IDs, or EFO trait labels. Returns variant details including rsIDs, p-values, mapped genes, and genomic locations. This is the best tool for finding all GWAS variants for a disease when you do NOT already have a specific variant ID.
GWAS search associations by gene
Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
gwas search associations
Search the GWAS Catalog for genome-wide association study results by keyword. Accepts free-text disease/trait names (e.g., 'melanoma', 'diabetes', 'breast cancer'), SNP rs IDs, EFO ontology IDs, or study accession IDs. This is the primary tool for discovering GWAS associations when you do NOT already have a specific association ID. Returns SNPs, p-values, odds ratios, mapped genes, and study metadata with pagination support.
gwas search snps
Search the GWAS Catalog for single nucleotide polymorphisms (SNPs) by rs ID (e.g., 'rs7903146') or mapped gene name (e.g., 'TCF7L2'). Returns SNP details including chromosomal location, mapped genes, and functional class. Use this to look up specific variants or find all GWAS-catalogued SNPs for a gene.
gwas search studies
Search for GWAS studies by various criteria including disease trait, cohort, GxE interactions, and summary statistics availability.
health disparities get county rankings info
Get information about County Health Rankings data. County Health Rankings provides county-level health data. This tool provides information about available datasets and access methods. Note: Data may be available as downloadable files or through their website.
health disparities get svi info
Get information about CDC Social Vulnerability Index (SVI) data. SVI data is typically available as downloadable CSV files from the CDC ATSDR website. This tool provides information about available SVI datasets and download links. Note: Actual data retrieval may require downloading CSV files.
HPO get term hierarchy
Get the parent or child terms of an HPO phenotype term in the ontology hierarchy. HPO is organized as a directed acyclic graph (DAG) where more specific phenotypes are children of broader terms. Use direction='children' to find more specific sub-phenotypes, or direction='parents' to find broader categories. Example: children of HP:0001250 (Seizure) include 'Bilateral tonic-clonic seizure', 'Focal-onset seizure', 'Febrile seizure', and others. Parents include 'Abnormal nervous system physiology'.
HPO get term
Get detailed information about a Human Phenotype Ontology (HPO) term by its ID. HPO provides standardized descriptions of phenotypic abnormalities in human disease with over 18,000 terms. Returns the term name, definition, synonyms, cross-references to UMLS/SNOMED, descendant count, and translations. Example: HP:0001250 (Seizure) returns definition, 346 descendants, synonyms including 'Epileptic seizure' and 'Epilepsy', and cross-references to UMLS and SNOMED-CT.
HPO search terms
Search for Human Phenotype Ontology (HPO) terms by keyword. HPO contains over 18,000 standardized phenotype terms used in clinical genetics and rare disease research. Returns matching terms with definitions, synonym counts, and descendant counts. Useful for finding the correct HPO ID for a clinical phenotype before querying disease or gene associations. Example: searching 'seizure' returns terms like 'Bilateral tonic-clonic seizure' (HP:0007334), 'Generalized-onset seizure' (HP:0002197), 'Foc...
icd search codes
Search for ICD-10 or ICD-11 codes using UMLS. Returns matching codes with descriptions. Requires free UMLS API key (register at https://uts.nlm.nih.gov/uts/). Set UMLS_API_KEY environment variable.
ICD10 get code info
Get detailed information about a specific ICD-10-CM code including full description, chapter, and category. ICD-10-CM codes are alphanumeric (e.g., E11.9 for Type 2 diabetes mellitus without complications). This tool provides the official code details from the 2026 ICD-10-CM release. No API key required (uses NLM Clinical Tables).
ICD10 search codes
Search ICD-10-CM (Clinical Modification) codes by disease name or code. ICD-10-CM is the US clinical modification of ICD-10, the current standard for diagnosis coding in US healthcare (effective through 2025). Returns matching codes with full descriptions. Uses NLM Clinical Tables API (no API key required). This provides 2026 ICD-10-CM codes for backward compatibility while ICD-11 adoption is ongoing.
ICD11 browse hierarchy
Navigate the ICD-11 disease classification hierarchy by retrieving child entities of a parent category. ICD-11 organizes diseases in a hierarchical tree structure (chapters → categories → subcategories). This tool returns all child entities under a specified parent, showing the disease classification taxonomy. Useful for exploring disease categories and understanding relationships. Requires ICD_CLIENT_ID and ICD_CLIENT_SECRET.
ICD11 get entity
Get detailed information about an ICD-11 disease entity by its unique identifier or code. Returns comprehensive details including full title, definition, inclusions, exclusions, parent/child relationships, diagnostic criteria, and clinical descriptions. Essential for understanding specific disease classifications. Requires ICD_CLIENT_ID and ICD_CLIENT_SECRET.
ICD11 search diseases
Search ICD-11 for diseases by name, symptoms, or clinical terms. ICD-11 is the WHO's 11th revision of the International Classification of Diseases, the global standard for diagnostic health information. Returns matching disease entities with codes, titles, and descriptions. Supports flexible search across 50+ languages. Requires ICD_CLIENT_ID and ICD_CLIENT_SECRET (register free at https://icd.who.int/icdapi).
IntOGen get drivers
Get cancer driver genes for a specific cancer type from IntOGen. Returns genes identified as drivers by computational methods (dNdScv, OncodriveFML, OncodriveCLUSTL, HotMAPS, smRegions, CBaSE, MutPanning) applied to somatic mutation data from thousands of tumors. Each result includes the gene symbol, number of mutations and mutated samples across cohorts. Use IntOGen_list_cancer_types to see available cancer type codes. Example: cancer_type='BRCA' returns 118 driver genes for breast cancer in...
IntOGen get gene info
Get driver gene classification for a specific gene across all cancer types from IntOGen. Returns the list of cancer types where the gene is identified as a cancer driver, along with the detection methods used (dNdScv, OncodriveFML, OncodriveCLUSTL, HotMAPS, smRegions, CBaSE, MutPanning) and mutation statistics. Example: gene='TP53' is a driver in 74 cancer types; gene='KRAS' is a driver in 22 cancer types.
IntOGen list cancer types
List all 87 cancer types available in IntOGen with their codes and full names. Returns cancer type identifiers (e.g., BRCA, LUAD, COADREAD, AML, SKCM) that can be used with IntOGen_get_drivers and IntOGen_list_cohorts. IntOGen covers 87 cancer types spanning solid tumors, hematological malignancies, and pediatric cancers.
IntOGen list cohorts
List available cancer cohorts from IntOGen with sample counts and tumor types. Returns cohort IDs, names, data sources (TCGA, ICGC, Hartwig, etc.), sample counts, tumor type (Primary/Metastasis), and age group (Adult/Pediatric). Optionally filter by cancer type. IntOGen includes 271 cohorts from major genomic studies. Example: cancer_type='BRCA' returns 14 breast cancer cohorts from TCGA, Hartwig, ICGC, and others.
IntentAnalyzerAgent
AI agent that analyzes user research intent and creates comprehensive search plans
kegg find genes
Find genes in KEGG database by keyword. Can search across all organisms or within a specific organism.
kegg get gene info
Get detailed gene information from KEGG by gene ID. Returns gene data including sequence, function, and pathway associations.
kegg get pathway info
Get detailed pathway information from KEGG by pathway ID. Returns pathway data including genes, compounds, and reactions.
kegg list organisms
List all available organisms in the KEGG database. Returns organism codes, names, and descriptions.
kegg search pathway
Search KEGG pathways by keyword. Returns pathway IDs and descriptions matching the search term.
KeywordExtractorAgent
AI agent that extracts and refines search keywords for research plans
LiteratureSynthesisAgent
AI agent that synthesizes literature findings and provides evidence-based insights
LOINC get answer list
Search LOINC answer-type codes matching a LOINC code or search term. Returns LOINC codes classified as answer-type items (categorical/coded result values used in clinical assessments). Use to find standardized answer codes for clinical observations.
LOINC get code details
Get detailed information for a specific LOINC code including full name, component, property, system, scale, method, and clinical classification. Use this to understand the precise meaning and context of a LOINC code obtained from lab results or clinical data.
loinc search codes
Search for LOINC (Logical Observation Identifiers Names and Codes) codes using UMLS. Returns matching codes with descriptions. Requires free UMLS API key (register at https://uts.nlm.nih.gov/uts/). Set UMLS_API_KEY environment variable.
LOINC search forms
Search LOINC clinical forms and survey instruments such as standardized questionnaires and assessment tools. Examples include PHQ-9 (depression), GAD-7 (anxiety), MMSE (cognitive), pain scales, and other validated clinical assessment instruments. Returns LOINC codes for complete forms that can be used in electronic health records.
LOINC search tests
Search LOINC (Logical Observation Identifiers Names and Codes) lab tests and clinical observations by name or keywords. Returns standardized codes for laboratory tests, vital signs, and clinical measurements. Essential for standardizing lab test names across healthcare systems and research studies.
MAGICapp get recommendations
Get all clinical recommendations from a specific MAGICapp guideline. Returns GRADE-rated recommendations with strength levels (STRONG, WEAK, PRACTICE, NO_STRENGTH), recommendation text (HTML), supporting remarks, rationale, and key information including evidence quality assessments. This is the core tool for accessing evidence-based clinical recommendations from living guidelines hosted on MAGICapp. Use MAGICapp_list_guidelines first to find guideline IDs.
MAGICapp get guideline
Get detailed information about a specific clinical guideline from MAGICapp by its numeric guideline ID. Returns comprehensive guideline metadata including title, authoring organization, contact information, version details, GRADE methodology settings, and links to PDF/JSON exports. Use MAGICapp_list_guidelines first to find guideline IDs, then use this tool to get full details. For the guideline's clinical recommendations, use MAGICapp_get_recommendations instead.
MAGICapp get sections
Get all sections (chapters) of a specific MAGICapp clinical guideline. Returns the structural organization of the guideline including section headings, text content, section types, and hierarchical ordering. Use this to understand the guideline's structure and find specific clinical topics within a guideline. Sections contain the narrative text while recommendations are accessed separately via MAGICapp_get_recommendations.
MAGICapp list guidelines
List all publicly available clinical guidelines from MAGICapp (Making GRADE the Irresistible Choice). MAGICapp hosts GRADE-based living guidelines from organizations like WHO, Stroke Foundation, American Dental Association, and others. Returns guideline metadata including name, owner organization, publication date, recommendation count, and guideline IDs for detailed lookups. Use this tool to discover available evidence-based clinical guidelines, then use MAGICapp_get_guideline or MAGICapp_ge...
MeSH get descriptor
Get detailed information for a MeSH descriptor by its ID. Returns the descriptor's label, type, annotation, tree numbers (for hierarchical browsing), date of introduction, and related terms. MeSH tree numbers encode the hierarchical position in the 16 MeSH categories (A=Anatomy, B=Organisms, C=Diseases, D=Chemicals, E=Analytical, etc.). Example: D009369 returns 'Neoplasms' with tree number C04, annotation about cancer terminology, and 'considerAlso' cross-references.
MeSH search descriptors
Search MeSH (Medical Subject Headings) descriptors by label. MeSH is NLM's controlled vocabulary for indexing biomedical literature in PubMed. Descriptors are the main headings in MeSH that represent biomedical concepts including diseases, drugs, anatomy, organisms, and procedures. Supports exact and contains matching. Example: searching 'Neoplasms' with exact match returns descriptor D009369.
MeSH search terms
Search MeSH terms (entry terms/synonyms) by label. MeSH terms include the preferred descriptor names as well as alternative entry terms, synonyms, and common names. This is broader than descriptor search and can find terms like 'heart attack' that map to the descriptor 'Myocardial Infarction'. Supports exact, contains, and startswith matching. Example: searching 'tumor' returns terms like 'Tumors', 'Tumor Growth', 'Tumors, Neoplastic'.
MedRxiv get preprint
Get full metadata for a specific medRxiv preprint by its DOI. Returns comprehensive metadata including title, authors, abstract, publication date, version, category, and URLs. Response time: <1 second. Use when you have a medRxiv DOI (format: 10.1101/YYYY.MM.DD.XXXXXXX). To SEARCH for medRxiv preprints by keywords, use EuropePMC_search_articles with 'SRC:PPR' filter (fast, relevance-ranked), or web_search with 'site:medrxiv.org'. medRxiv API does not support text search.
MedlinePlus connect lookup by code
Look up corresponding MedlinePlus page information through MedlinePlus Connect Web Service using clinical/drug/test codes (such as ICD-10 CM, RXCUI, LOINC, etc.), supports JSON or XML format return.
MedlinePlus get genetics condition by name
Get detailed information from MedlinePlus Genetics corresponding to genetic condition name. Returns XML data parsed into a dictionary with condition description, related genes, synonyms, and other details.
MedlinePlus get genetics index
Download index file (XML) of all genetics entries in MedlinePlus, get complete list in one call.
MedlinePlus get genetics gene by name
Get detailed information from MedlinePlus Genetics corresponding to gene name. Returns XML data parsed into a dictionary with gene function, related health conditions, synonyms, and other details.
MedlinePlus search topics by keyword
Search for relevant information in MedlinePlus Web Service by keyword across health topics or other sub-libraries (such as drugs, genetics, etc.).
Mondo get disease phenotypes
Get HPO (Human Phenotype Ontology) phenotypes associated with a Mondo disease. Returns the phenotype IDs (HP:xxxxxxx), names, and the specific disease subtype contributing each phenotype. Data comes from OMIM, Orphanet, and clinical annotations. Use this to understand clinical presentations and symptoms of a disease. First find the Mondo ID using Mondo_search_disease, then query phenotypes here.
Mondo get disease
Get detailed information about a disease from the Mondo Disease Ontology by its MONDO ID. Returns the disease name, description, synonyms, cross-references (OMIM, Orphanet, DOID, MeSH, ICD-10, NCIT, UMLS, SNOMED-CT), hierarchy (parent diseases), subtypes count, causal genes, inheritance pattern, and association counts (phenotypes, correlated genes, etc.). Essential for understanding disease classification and finding equivalent IDs across ontologies.
Mondo search disease
Search the Mondo Disease Ontology for diseases by name or keyword. Mondo unifies disease identifiers across OMIM, Orphanet, DOID, MeSH, ICD-10, NCIT, and other ontologies into a single MONDO ID. Returns matching disease entries with their Mondo IDs, descriptions, and cross-references. Use this to find the Mondo ID for a disease before querying Mondo_get_disease or Mondo_get_disease_phenotypes. Examples: 'Alzheimer' returns MONDO:0004975, 'breast cancer' returns MONDO:0007254, 'diabetes' retur...
MultiAgentLiteratureSearch
Multi-agent literature search system that uses AI agents to analyze intent, extract keywords, execute parallel searches, summarize results, and check quality iteratively
NCA calculate bioavailability
Calculate absolute oral bioavailability (F) from paired IV and PO pharmacokinetic study AUC values and doses. Formula: F = (AUC_PO × Dose_IV) / (AUC_IV × Dose_PO). Classifies result as High (≥80%), Moderate (30–80%), Low (10–30%), or Very Low (<10%) with clinical interpretation. F > 20% is typically considered acceptable for small molecule oral drugs. F ≥ 80% required for bioequivalence. Use after NCA_compute_parameters to calculate AUC from raw time-concentration data for both IV and PO arms.
NCA compute parameters
Perform Non-Compartmental Analysis (NCA) on time-concentration pharmacokinetic data. Computes key PK parameters: Cmax (peak concentration), Tmax (time to peak), AUC0-t (area under curve to last measured point using linear-log trapezoidal method), AUC0-inf (extrapolated), terminal elimination half-life (t½), elimination rate constant (λz), clearance (CL), and volume of distribution (Vd) when dose is provided. Follows FDA/EMA NCA guidelines. Use this when you have raw plasma concentration vs. t...
NCA fit one compartment
Fit a one-compartment IV bolus pharmacokinetic model (C(t) = C0 × exp(-k_el × t)) to plasma concentration-time data using nonlinear least squares. Returns C0 (initial concentration), k_el (elimination rate constant), t½ (half-life), R², and when dose is provided: Vd (volume of distribution) and CL (clearance). Assumes mono-exponential decline — appropriate for drugs with rapid distribution and linear elimination. If R² < 0.85, consider a two-compartment model. Use NCA_compute_parameters for m...
NCCN get patient guideline
Fetch content from a specific NCCN Guidelines for Patients page. Takes a URL obtained from NCCN_list_patient_guidelines and scrapes the page for title, content sections, and PDF download links. Returns the guideline page content organized by sections. Note: NCCN patient guidelines are educational summaries; for full professional guidelines, use NCCN_search_guidelines to find JNCCN publications.
NCCN search guidelines
Search NCCN (National Comprehensive Cancer Network) guidelines and publications via PubMed. Searches the JNCCN (Journal of the NCCN) and other NCCN publications for clinical practice guidelines, evidence blocks, and discussion papers on cancer treatment. Useful for finding specific NCCN treatment recommendations and updates.
NCCN list patient guidelines
List all NCCN (National Comprehensive Cancer Network) Guidelines for Patients available on nccn.org. These are free, publicly accessible cancer treatment guides organized by cancer type, detection/prevention, supportive care, and specific populations. Returns cancer type names, URLs, and category. Over 70 cancer types are covered including breast, lung, colon, prostate, melanoma, leukemias, and lymphomas.
NCI expand drugs by letter
Browse the NCI Drug Dictionary by first letter. Returns all cancer drugs and drug aliases starting with the specified letter. Each result includes the drug name, preferred name, type (DrugTerm or DrugAlias), and a pretty URL name for detailed lookups. Useful for discovering cancer drugs alphabetically or finding all drugs starting with a specific letter. Use NCI_get_drug_by_name with the prettyUrlName to get full details.
NCI get drug by name
Get detailed information about a cancer drug from the NCI Drug Dictionary by its pretty-url-name (slug). Returns comprehensive drug information including definition, aliases (brand names, chemical names, code names, CAS registry numbers), NCI concept ID, and links to drug information summaries. The pretty-url-name is a lowercase hyphenated slug (e.g., 'pembrolizumab', 'tamoxifen-citrate', 'nivolumab'). You can find drug names from NCIDrugDict_search results (prettyUrlName field).
NCI search cancer resources
Search NCI (National Cancer Institute) Resources for Researchers (R4R) for cancer research tools, databases, datasets, and clinical research resources. The R4R collection includes bioinformatics tools, clinical research tools, lab instruments, datasets, specimen repositories, and community resources. Returns resource descriptions, links, tool types, research areas, and research types. Useful for finding cancer-specific research resources, analysis tools, and clinical resources.
nhanes get dataset info
Get information about NHANES (National Health and Nutrition Examination Survey) datasets. NHANES data is typically available as downloadable files (SAS, XPT formats) from the CDC website. This tool provides information about available datasets, years, and download links. Note: Actual data retrieval may require downloading and converting files.
nhanes search datasets
Search for NHANES datasets by keyword. Returns information about matching datasets including download links. Note: NHANES data files are typically in SAS/XPT format and may require conversion tools.
NICE Clinical Guidelines Search
Search NICE (National Institute for Health and Care Excellence) clinical guidelines and evidence-based recommendations. Provides access to official NICE guidelines covering diagnosis, treatment, and care pathways for various medical conditions.
NICE Guideline Full Text
Fetch complete full text content from a NICE clinical guideline page. Takes a NICE guideline URL and extracts all sections, recommendations, and complete guideline text. Use this after finding a guideline with NICE_Clinical_Guidelines_Search to get the full content.
odphp itemlist
This tools browses and returns available topics and categories and it is helpful to help narrow a broad request (e.g., “show me all topics”). For full topic content, `odphp_topicsearch` tool is helpful.
odphp outlink fetch
This tool retrieves readable text from ODPHP article links and information sources. This is helpful after using the `odphp_myhealthfinder` or `odphp_topicsearch` tools or when the user wants to simply dive deeper into ODPHP data.
odphp myhealthfinder
This tool provides personalized preventive-care recommendations and it is helpful for different ages, sexes, pregnancy status, gives age/sex/pregnancy. It retrieves metadata, plain-language sections, and dataset links to the full article (AccessibleVersion links). If the user wants the full text of a recommendation, the `odphp_outlink_fetch` tool is helpful.
odphp topicsearch
Find specific health topics and get their full content. Use when the user mentions a keyword (e.g., “folic acid”, “blood pressure”) or when you already have topic/category IDs from `odphp_itemlist`. Returns detailed topic pages (Title, Sections, RelatedItems) and an AccessibleVersion link. Next: to quote or summarize the actual page text, pass the AccessibleVersion (or RelatedItems URLs) to `odphp_outlink_fetch`.
OMIM get clinical synopsis
Get clinical synopsis (phenotype features) for an OMIM phenotype entry. Returns structured clinical features organized by body system (e.g., neurologic, cardiovascular). Essential for phenotype-based disease matching. Requires OMIM_API_KEY.
OMIM get entry
Get detailed OMIM entry by MIM number. Returns comprehensive information including text description, clinical features, inheritance, molecular genetics, and references. MIM numbers are 6-digit identifiers (e.g., 164730 for BRAF gene). Requires OMIM_API_KEY.
OMIM get gene map
Get OMIM gene-disease mapping information. Returns genes mapped to chromosomal locations with associated phenotypes and inheritance patterns. Query by MIM number or chromosome. Useful for finding all disease genes on a chromosome.
OMIM search
Search OMIM database for Mendelian diseases and genes. OMIM is the authoritative source for human genetic disorders. Search by gene name, disease name, or phenotype keywords. Returns MIM numbers, titles, and entry types. Requires OMIM_API_KEY env var (register at omim.org/api).
OncoKB annotate copy number
Annotate copy number alterations (amplification/deletion) for oncogenic potential. Returns evidence for gene amplification or deletion in cancer. Example: ERBB2 amplification in breast cancer, CDKN2A deletion.
OncoKB get cancer genes
Get list of all cancer genes curated in OncoKB. Returns genes classified as oncogenes and/or tumor suppressors. Useful for checking if a gene is a known cancer driver. Requires ONCOKB_API_TOKEN env var.
OncoKB get gene info
Get gene-level oncogenic information from OncoKB. Returns whether gene is an oncogene, tumor suppressor, or both. Includes curated background information. Requires ONCOKB_API_TOKEN env var (demo mode available for BRAF, TP53, ROS1).
OncoKB get levels
Get OncoKB evidence level definitions. Returns descriptions of all therapeutic actionability levels (1, 2, 3A, 3B, 4, R1, R2). Level 1 = FDA-approved, Level 2 = Standard care, Level 3A = Compelling clinical evidence, etc.
OncoKB annotate variant
Annotate a cancer variant for oncogenic potential and treatment implications using OncoKB. Returns evidence level, oncogenicity, mutation effect, and FDA-approved therapies. Requires ONCOKB_API_TOKEN env var (demo mode available for BRAF, TP53, ROS1). Example: BRAF V600E in melanoma.
OpenAlex Guidelines Search
Search for clinical practice guidelines using OpenAlex scholarly database. Provides access to a comprehensive collection of guidelines from various sources worldwide, with citation metrics and institutional affiliations.
OpenFDA search device 510k
Search the FDA 510(k) premarket notification database via openFDA. Contains clearances for medical devices through the 510(k) pathway (substantial equivalence). Returns device names, applicant companies, decision dates, advisory committee classifications, and FDA decision types. Useful for medical device research, competitive landscape analysis, and understanding regulatory pathways for specific device categories.
OpenFDA search device enforcement
Search the FDA medical device enforcement (recall) database via openFDA. Contains medical device recalls, corrections, and removals. Use Lucene query syntax: 'classification:"Class I"' (most serious), 'status:Ongoing', 'recalling_firm:"Medtronic"'. Returns recall details including product description, reason for recall, and distribution pattern. Medical devices include implants, diagnostic equipment, surgical tools, and consumer medical devices.
OpenFDA search drug enforcement
Search the FDA drug enforcement (recall) database via openFDA. Contains drug recalls, withdrawals, and field corrections submitted to the FDA. Use Lucene query syntax: 'classification:"Class I"' (most serious, may cause death), 'recalling_firm:pfizer', 'status:Ongoing'. Returns recall details including reason, product description, distribution pattern, classification, firm, and dates. Use count parameter for frequency analysis (e.g., count='classification' to see recall counts by class).
OpenFDA search drug labels
Search the FDA drug label (SPL - Structured Product Labeling) database via openFDA. Contains approved prescription and OTC drug labels including indications, warnings, dosage, adverse reactions, contraindications, and pharmacology sections. Use Lucene query syntax: 'openfda.brand_name:aspirin', 'openfda.generic_name:ibuprofen', 'openfda.manufacturer_name:pfizer'. Returns label text sections and openFDA cross-references (brand name, generic name, substance name, product type).
OpenFDA search drug events
Search the FDA Adverse Event Reporting System (FAERS) database via openFDA for drug safety reports. Contains 20+ million adverse event reports submitted to the FDA. Use Lucene syntax: 'patient.drug.medicinalproduct:aspirin', 'patient.reaction.reactionmeddrapt:headache'. Returns serious adverse events with outcomes (hospitalization, death), suspect drugs, and reported reactions using MedDRA terminology.
OpenFDA search drug ndc
Search the FDA National Drug Code (NDC) Directory via openFDA. The NDC directory identifies drugs listed under Section 510 of the FDA Act, covering finished dosage forms, unfinished APIs, and non-prescription drugs. Returns product/package codes, brand/generic names, dosage forms, routes of administration, active ingredients, and marketing information.
OpenFDA search food enforcement
Search the FDA food enforcement (recall) database via openFDA. Contains food recalls, market withdrawals, and safety alerts. Use Lucene query syntax: 'classification:"Class I"' (most serious), 'status:Ongoing', 'recalling_firm:"Company Name"'. Returns recall details including product description, reason for recall, distribution pattern, and classification. Useful for food safety research, supply chain analysis, and identifying contamination patterns.
OpenTargets drug pharmacogenomics data
Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annotations.
OpenTargets get approved indications by drug chemblId
Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.
OpenTargets get associated diseases by drug chemblId
Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial data or post-marketed drugs.
OpenTargets get associated drugs by disease efoId
Retrieve known drugs associated with a specific disease by disease efoId.
OpenTargets get associated drugs by target ensemblID
Get known drugs and information (e.g. id, name, MoA) associated with a specific target ensemblID, including clinical trial phase and mechanism of action of the drugs.
OpenTargets get associated phenotypes by disease efoId
Find HPO phenotypes asosciated with the specified disease efoId.
OpenTargets get associated targets by disease efoId
Find targets associated with a specific disease or phenotype based on efoId.
OpenTargets get associated targets by drug chemblId
Retrieve the list of targets linked to a specific drug chemblId based on its mechanism of action.
OpenTargets get biological mouse models by ensemblID
Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a specific target.
OpenTargets get chemical probes by target ensemblID
Retrieve chemical probes associated with a specific target using its ensemblID.
OpenTargets get credible set detail
Get detailed information about a specific GWAS credible set (fine-mapped locus) from Open Targets. Returns the lead variant, associated study, fine-mapping method, statistical significance, locus-to-gene (L2G) predictions mapping the signal to likely causal genes, and colocalization evidence with QTLs.
OpenTargets get disease ancestors parents by efoId
Retrieve the disease ancestors and parents in the ontology using the disease EFO ID.
OpenTargets get disease descendants children by efoId
Retrieve the disease descendants and children in the ontology using the disease EFO ID.
OpenTargets get disease description by efoId
Retrieve disease description, name, database cros references, obsolete terms, and whether it's a therapeutic area, all using the specified efoId.
OpenTargets get disease id description by name
Retrieve the efoId and additional details of a disease based on its name.
OpenTargets get disease locations by efoId
Retrieve the disease's direct location and indirect location disease terms and IDs using the disease EFO ID.
OpenTargets get disease synonyms by efoId
Retrieve disease synonyms by its EFO ID.
OpenTargets get disease therapeutic areas by efoId
Retrieve the therapeutic areas associated with a specific disease efoId.
OpenTargets get diseases phenotypes by target ensembl
Find diseases or phenotypes associated with a specific target using ensemblId.
OpenTargets get drug adverse events by chemblId
Retrieve significant adverse events reported for a specific drug chemblId.
OpenTargets get drug approval status by chemblId
Retrieve the approval status of a specific drug chemblId.
OpenTargets get drug blackbox status by chembl ID
Find withdrawn and black-box warning statuses for a specific drug by chemblId.
OpenTargets get drug chembId by generic name
Fetch the drug chemblId and description based on the drug generic name.
OpenTargets get drug description by chemblId
Get drug name, year of first approval, type, cross references, and max clinical trial phase based on specified chemblId.
OpenTargets get drug id description by name
Fetch the drug chemblId and description based on the drug generic name.
OpenTargets get drug indications by chemblId
Fetch indications (treatable phenotypes/diseases) for a given drug chemblId.
OpenTargets get drug mechanisms of action by chemblId
Retrieve the mechanisms of action associated with a specific drug using chemblId.
OpenTargets get drug names by chemblId
Get drug generic name and brand names (trade names) based on ChEMBL ID. Returns the drug name (typically generic name), trade names (brand names), and synonyms.
OpenTargets get drug synonyms by chemblId
Retrieve the synonyms associated with a specific drug chemblId.
OpenTargets get drug trade names by chemblId
Retrieve the trade names associated with a specific drug chemblId.
OpenTargets get drug warnings by chemblId
Retrieve warnings for a specific drug using ChEMBL ID.
OpenTargets get evidence by datasource
Get target-disease evidence from Open Targets filtered by configurable data sources. Unlike OpenTargets_target_disease_evidence (intogen-only), this tool accepts any datasourceIds. Valid sources include: ot_genetics_portal, eva, eva_somatic, gene_burden, genomics_england, intogen, cancer_gene_census, chembl, crispr, europepmc, expression_atlas, gene2phenotype, orphanet, uniprot_literature, uniprot_variants, clingen, phewas_catalog, reactome, progeny, slapenrich, sysbio. Returns evidence rows ...
OpenTargets get gene ontology terms by goID
Retrieve Gene Ontology terms based on a list of GO IDs.
OpenTargets get gwas study
Get detailed metadata for a GWAS study from Open Targets Platform, including trait information, sample sizes, publication details, disease mappings, cohorts, LD population structure, and availability of summary statistics. Use GCST accession IDs.
OpenTargets get known drugs by drug chemblId
Get a list of known drugs and associated information using the specified chemblId.
OpenTargets get parent child molecules by chembl ID
Get parent and child molecules of specified drug chemblId.
OpenTargets get publications by disease efoId
Retrieve publications related to a disease efoId, including PubMed IDs and publication dates.
OpenTargets get publications by drug chemblId
Retrieve publications related to a drug chemblId, including PubMed IDs and publication dates.
OpenTargets get publications by target ensemblID
Retrieve publications related to a target ensemblID, including PubMed IDs and publication dates.
OpenTargets get similar entities by disease efoId
Retrieve similar entities for a given disease efoId using a model trained with PubMed.
OpenTargets get similar entities by drug chemblId
Retrieve similar entities for a given drug chemblId using a model trained with PubMed.
OpenTargets get similar entities by target ensemblID
Retrieve similar entities for a given target ensemblID using a model trained with PubMed.
OpenTargets get study credible sets
Get all credible sets (fine-mapped GWAS loci) for a specific GWAS study from Open Targets. Returns the lead variants, fine-mapping details, p-values, effect sizes, and locus-to-gene (L2G) predictions for each locus in the study. Use this to explore all significant loci discovered in a GWAS.
OpenTargets get target classes by ensemblID
Retrieve the target classes associated with a specific target ensemblID.
OpenTargets get target constraint info by ensemblID
Retrieve genetic constraint information for a specific target ensemblID, including expected and observed values, and scores.
OpenTargets get target enabling packages by ensemblID
Retrieve the Target Enabling Packages (TEP) associated with a specific target ensemblID.
OpenTargets get target gene ontology by ensemblID
Retrieve Gene Ontology annotations for a specific target by Ensembl ID.
OpenTargets get target genomic location by ensemblID
Retrieve genomic location data for a specific target, including chromosome, start, end, and strand.
OpenTargets get target homologues by ensemblID
Fetch homologues for a specific target by Ensembl ID.
OpenTargets get target id description by name
Get the ensemblId and description based on the target name.
OpenTargets get target safety profile by ensemblID
Retrieve known target safety liabilities for a specific target Ensembl ID.
OpenTargets get target interactions by ensemblID
Retrieve interaction data for a specific target ensemblID, including interaction partners and evidence.
OpenTargets get target subcell locations by ensembl ID
Retrieve information about subcellular locations for a specific target ensemblID.
OpenTargets get target synonyms by ensemblID
Retrieve synonyms for specified target, including alternative names and symbols, using given ensemblID.
OpenTargets get target tractability by ensemblID
Retrieve tractability assessments, including modality and values, for a specific target ensembl ID.
OpenTargets get variant credible sets
Get GWAS credible sets (fine-mapped loci) associated with a genetic variant from Open Targets. Returns studies where this variant appears in a fine-mapped credible set, with locus-to-gene (L2G) predictions, p-values, effect sizes, and the fine-mapping method used. Essential for understanding which GWAS signals a variant is part of and which genes it likely affects.
OpenTargets get variant info
Get detailed information about a genetic variant from Open Targets Platform, including genomic coordinates, rsIDs, allele frequencies across populations (gnomAD), functional consequence, transcript consequences, and HGVS notation. Useful for GWAS variant annotation and population genetics.
OpenTargets multi entity search by query string
Perform a multi-entity search based on a query string, filtering by entity names and pagination settings.
OpenTargets search category counts by query string
Get the count of entries in each entity category (disease, target, drug) based on a query string.
OpenTargets search gwas studies by disease
Search for GWAS studies associated with a disease or trait in Open Targets. Takes disease ontology IDs (EFO, MONDO) and returns matching GWAS studies with their metadata including sample sizes, traits, publications, and associated diseases. Use enableIndirect=true to include child disease terms.
OpenTargets target disease evidence
Explore IntOGen somatic driver evidence for a target-disease association (cancer mutation data only). For broader evidence across all data sources (genetics, literature, pathways, etc.), use OpenTargets_get_evidence_by_datasource instead. Input is disease efoId and target ensemblID.
openalex get author
Get a single OpenAlex author by Author ID (A...). You can pass either the short ID (e.g., "A5001226970") or the full URL (e.g., "https://openalex.org/A5001226970").
openalex get institution
Get a single OpenAlex institution by Institution ID (I...). You can pass either the short ID (e.g., "I136199984") or the full URL (e.g., "https://openalex.org/I136199984").
openalex get work by doi
Get a single OpenAlex work (paper) by DOI. Provide a DOI string like "10.65215/2q58a426" (you can also pass a DOI URL like "https://doi.org/10.65215/2q58a426").
openalex get work
Get a single OpenAlex work (paper) by OpenAlex Work ID (W...). You can pass either the short ID (e.g., "W2626778328") or the full URL (e.g., "https://openalex.org/W2626778328").
openalex literature search
Search for academic literature using OpenAlex. Supports optional full-text-index filtering (has_fulltext + fulltext.search) when you need body-only term discovery, but note: OpenAlex full-text indexing is incomplete, and a work can be open-access elsewhere (e.g., PMC) while still having has_fulltext=false in OpenAlex. Returns paper metadata and (when available) OA links/content URLs.
openalex search authors
Search OpenAlex authors via the /authors endpoint. Use this to discover Author IDs (A...) and then fetch details with openalex_get_author.
openalex search institutions
Search OpenAlex institutions via the /institutions endpoint. Use this to discover Institution IDs (I...) and then fetch details with openalex_get_institution.
openalex search works
Search OpenAlex works (papers) via the /works endpoint. Supports both general search and optional full-text-index filtering: set require_has_fulltext=true and/or pass fulltext_terms to add OpenAlex filters (has_fulltext:true and fulltext.search:<term>). Important: has_fulltext/fulltext.search only match works where OpenAlex has indexed full text; this can miss papers whose full text is available elsewhere (e.g., PMC) but not indexed by OpenAlex. Use this to discover Work IDs (W...) and DOIs, ...
Orphanet get classification
Get disease classification hierarchy from Orphanet. Returns parent and child disease categories showing where a disease fits in the rare disease taxonomy. Useful for understanding disease relationships.
Orphanet get disease
Get detailed information about a rare disease by ORPHA code. Returns disease name, definition, synonyms, and classification. ORPHA codes are unique Orphanet identifiers (e.g., 558 for Marfan syndrome). No authentication required.
Orphanet get epidemiology
Get epidemiology data (prevalence, incidence) for a rare disease from Orphanet. Returns prevalence estimates by geographic region and type (point prevalence, birth prevalence, annual incidence). Data includes validation status and literature sources.
Orphanet get gene diseases
Get rare diseases associated with a gene from Orphanet. Accepts gene symbols (e.g., 'FBN1', 'BRCA1', 'HTT') or gene name keywords (e.g., 'fibrillin', 'huntingtin', 'dystrophin'). Gene symbols are auto-resolved to full names. Returns disease ORPHA codes, gene symbols, association types, and genomic locus information.
Orphanet get genes
Get genes associated with a rare disease from Orphanet. Returns gene symbols, names, and association types (causative, modifier, susceptibility). Essential for rare disease genetic diagnosis.
Orphanet get icd mapping
Get cross-references between Orphanet ORPHA codes and other medical coding systems (ICD-10, ICD-11, OMIM, SNOMED-CT). Essential for mapping rare disease codes across clinical and research nomenclatures. Returns mapping relationships and validation status.
Orphanet get natural history
Get natural history data for a rare disease from Orphanet. Returns average age of onset and type of inheritance. Useful for understanding disease progression patterns and genetic counseling.
Orphanet get phenotypes
Get HPO (Human Phenotype Ontology) phenotypes associated with a rare disease from Orphanet. Returns HPO terms with their frequency (Very frequent, Frequent, Occasional, Very rare, Excluded) and whether they are diagnostic criteria. Essential for phenotype-driven rare disease diagnosis.
Orphanet search by name
Search for rare diseases by exact or partial name match in Orphanet. More precise than keyword search. Returns ORPHA codes and disease names. Supports exact matching mode for disambiguation.
Orphanet search diseases
Search Orphanet for rare diseases by keyword. Orphanet is the reference portal for rare diseases and orphan drugs. Returns disease names, ORPHA codes, and synonyms. No authentication required. Supports multiple languages (en, fr, de, es, it, pt, pl, nl).
OverallSummaryAgent
AI agent that generates comprehensive overall summary of multi-agent search results
PanelApp get panel
Get the full gene list and details for a specific Genomics England PanelApp gene panel by panel ID. Returns all genes in the panel with their confidence levels (3=green/diagnostic, 2=amber/borderline, 1=red/limited), mode of inheritance, mode of pathogenicity, penetrance, phenotypes, publications, and evidence sources. This is the definitive resource for which genes are included in clinical genetic testing panels used by the NHS. Use PanelApp_search_panels to find panel IDs.
PanelApp search genes
Search for a gene across all Genomics England PanelApp panels to find which clinical testing panels include it. Returns all panels containing the gene, along with the confidence level, mode of inheritance, and associated phenotypes for each panel. This is invaluable for understanding the clinical significance of a gene - if it appears in multiple high-confidence panels, it has strong clinical evidence. Use gene symbols (e.g., 'TP53', 'BRCA1').
PanelApp search panels
Search Genomics England PanelApp for gene panels used in clinical genetic testing. PanelApp is the authoritative source for curated gene panels used by the NHS and global genomic medicine services. Returns panel IDs, names, disease groups, status, version, and gene count statistics. Use this to find relevant gene panels for a disease area, then use PanelApp_get_panel to get the full gene list. Panels contain genes with confidence levels (green=3 for diagnostic grade, amber=2 for borderline, r...
PharmGKB get clinical annotations
Get clinical annotations showing gene-drug-phenotype relationships. Returns variant-level clinical significance data. Always provide a specific 'annotation_id' — filtering by gene_id is unreliable and may return empty results.
PharmGKB get dosing guidelines
Get pharmacogenetic dosing guidelines (CPIC/DPWG) from PharmGKB by guideline_id. IMPORTANT: use the 'clinpgxid' field from CPIC_list_guidelines (e.g., 'PA166251454'), NOT the 'pharmgkbid' field — old-format pharmgkbid values (e.g., 'PA166104996') return HTTP 404. The test example PA166251465 is for the warfarin guideline.
PharmGKB get drug details
Get detailed information for a drug using its PharmGKB Chemical ID. Returns structural info, cross-references, and related genes.
PharmGKB get gene details
Get detailed information for a gene using its PharmGKB Accession ID. Returns chromosomal location, cross-references, and other metadata.
PharmGKB search drugs
Search for drugs in PharmGKB by name or PharmGKB ID. Returns drug name, ID, and basic metadata.
PharmGKB search genes
Search for genes in PharmGKB by name, symbol, or ID. Returns PharmGKB Gene ID and basic gene metadata.
PharmGKB search variants
Search for genetic variants in PharmGKB by rsID or name. Returns variant IDs and associated gene info.
PharmacoDB get biomarker assoc
Get gene-compound biomarker associations from PharmacoDB showing how gene expression or other molecular features correlate with drug sensitivity. Returns statistical associations including effect estimate, p-values, FDR, sensitivity statistic (AAC/IC50), molecular data type (rna/cnv/mutation), sample size, and tissue/dataset context. Filter by compound, gene (Ensembl ID), tissue, and molecular data type. Useful for pharmacogenomics biomarker discovery and validating drug sensitivity predictor...
PharmacoDB get compound
Get detailed information about a compound/drug from PharmacoDB, including chemical annotations (SMILES, InChIKey, PubChem CID, ChEMBL ID, FDA approval status), the datasets it has been profiled in, and its known molecular targets with associated genes. Look up by compound name or PharmacoDB compound ID. Useful for characterizing drug properties and identifying which pharmacogenomics datasets include a specific compound. Example: get details for Paclitaxel, Erlotinib, or Lapatinib.
PharmacoDB get cell line
Get detailed information about a cancer cell line from PharmacoDB, including tissue of origin, disease annotations, dataset-specific synonyms, and accession IDs. Look up by cell line name or PharmacoDB cell ID. PharmacoDB harmonizes cell line identifiers across 10 pharmacogenomics datasets. Example: get details for MCF-7 breast cancer or A549 lung cancer cell line.
PharmacoDB get experiments
Get drug sensitivity experiments from PharmacoDB with dose-response curves and pharmacological profiles. Returns experiment data including raw dose-response measurements and fitted parameters (IC50, EC50, AAC, Hill slope, Einf, DSS1/2/3). Filter by compound name, cell line name, and/or dataset. Integrates data from CCLE, CTRPv2, FIMM, GDSC1, GDSC2, GRAY, NCI60, PRISM, UHNBreast, and gCSI. Essential for comparing drug sensitivity across cell lines and datasets. Example: get Paclitaxel dose-res...
PharmacoDB list datasets
List all cancer pharmacogenomics datasets available in PharmacoDB. Returns dataset names and IDs for the integrated collection including CCLE (Cancer Cell Line Encyclopedia), CTRPv2 (Cancer Therapeutics Response Portal), FIMM (Institute for Molecular Medicine Finland), GDSC1/GDSC2 (Genomics of Drug Sensitivity in Cancer), GRAY, NCI60, PRISM, UHNBreast, and gCSI (Genentech Cell Screening Initiative). Use dataset names to filter experiments and biomarker queries.
PharmacoDB search
Search PharmacoDB for compounds, cell lines, tissues, or genes by name. PharmacoDB integrates cancer pharmacogenomics data from 10 major datasets (CCLE, CTRPv2, FIMM, GDSC1, GDSC2, GRAY, NCI60, PRISM, UHNBreast, gCSI). Returns matching entities with their PharmacoDB UIDs and type (compound, cell_line, tissue, gene). Use this to find PharmacoDB identifiers for use with other PharmacoDB tools. Example: search for 'paclitaxel' to find its PharmacoDB compound ID.
PubChem get assay active compounds
Get CIDs of compounds that are ACTIVE in a bioassay. Returns compound IDs that passed the activity threshold. Use for hit identification from HTS screens.
PubChem get assay description
Get bioassay description and metadata by AID. Returns assay name, source, protocol, target information, activity outcomes, and data columns. Essential for understanding what an assay measures before retrieving results.
PubChem get assay dose response
Get dose-response data from a bioassay. Returns concentration-response curves for tested compounds. Essential for determining IC50/EC50 values. Limited to dose-response type assays.
PubChem get assay targets
Get protein/gene targets for a bioassay. Returns GI numbers, protein names, gene IDs, and gene symbols. Critical for understanding what molecular targets an assay screens against.
PubChem get assays for compound active
Get AIDs of assays where a compound is ACTIVE. Returns list of bioassay IDs where the compound showed activity. Use to understand a compound's target profile.
PubChem get assay summary
Get summary statistics for a bioassay by AID. Returns counts of active/inactive compounds, target information, and assay metadata. Useful for quick assessment of assay size and hit rate.
PubChem get associated patents by CID
Get a list of patents associated with a specific compound CID.
PubChem get CID by compound name
Search PubChem by compound name to get CID(s). This is the PRIMARY tool for looking up a drug or chemical by name (e.g., 'cytarabine', 'aspirin', 'metformin', 'venetoclax') to obtain PubChem Compound IDs. Use the returned CID with other PubChem tools for properties, patents, etc. Only works with chemical/drug names, not disease names.
PubChem get CID by SMILES
Retrieve corresponding CID list by SMILES string.
PubChem get compound 2D image by CID
Get 2D structure image (PNG format) of compound by CID.
PubChem get compound bioactivity
Get bioassay results summary for a compound by CID. Returns all assays the compound was tested in, activity outcomes (active/inactive), and target information. Critical for understanding compound's biological profile.
PubChem get compound properties by CID
Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, IUPAC name, Canonical SMILES.
PubChem get compound synonyms by CID
Get complete list of synonyms for compound by CID.
PubChem get compound xrefs by CID
Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.
PubChem search compounds by similarity
Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above threshold to given SMILES molecule. Returns up to max_results CIDs (default 10).
PubChem search assays by target gene
Search bioassays by target gene symbol. Returns AIDs of assays that screen against the specified gene. Example: USP2 returns assays targeting USP2 protease.
PubChem search assays by type
Search bioassays by assay type. Types: screening (HTS), confirmatory, doseresponse, summary, cellbased, biochemical, invivo, invitro. Returns list of matching AIDs.
PubChem search compounds by substructure
Search for CIDs in PubChem that contain the given substructure (SMILES). Returns up to max_results CIDs (default 10).
PubChemTox get acute effects
Get acute toxicity effects for a chemical compound from PubChem. Returns documented acute (short-term) health effects from exposure, including symptoms, clinical observations, and effects from different exposure routes (oral, inhalation, dermal). Data comes from toxicological databases and clinical case reports. For example, arsenic acute effects include severe gastrointestinal damage, cardiovascular collapse, and multi-organ failure. Methanol (CID 887) causes visual disturbances, metabolic a...
PubChemTox get carcinogen classification
Get carcinogen classification data for a chemical compound from PubChem. Returns classifications from authoritative bodies including IARC (International Agency for Research on Cancer), NTP (National Toxicology Program), EPA, and others. IARC groups: Group 1 (Carcinogenic to humans), Group 2A (Probably carcinogenic), Group 2B (Possibly carcinogenic), Group 3 (Not classifiable). For example, arsenic (CID 5359596) is IARC Group 1 (Carcinogenic to humans), benzene (CID 241) is also Group 1, while...
PubChemTox get ghs classification
Get GHS (Globally Harmonized System) hazard classification for a chemical compound from PubChem. Returns hazard pictograms, signal words (Danger/Warning), GHS hazard statements (e.g., H301 'Toxic if swallowed'), and precautionary statements. GHS is the UN system for identifying hazardous chemicals. Can look up by PubChem CID or compound name. For example, arsenic (CID 5359596) has pictograms for Acute Toxic and Environmental Hazard with signal word 'Danger', while aspirin (CID 2244) has signa...
PubChemTox get target organs
Get the target organs affected by a toxic chemical compound from PubChem. Returns the organs and body systems known to be damaged by exposure to the chemical, based on toxicological studies and clinical evidence. For example, arsenic (CID 5359596) targets cardiovascular, dermal, endocrine, gastrointestinal, hematological, neurological, and renal systems, as well as liver, kidneys, skin, lungs, and lymphatic system. Lead (CID 5352425) primarily targets the nervous system, kidneys, and hematolo...
PubChemTox get toxicity summary
Get a comprehensive toxicity data summary for a chemical compound from PubChem. Returns an overview of all available toxicity data sections and subsections, including previews of each data type. This acts as a table of contents for all toxicological data available in PubChem for a compound. Sections include: Toxicological Information (EPA IRIS, hepatotoxicity, carcinogen classification, exposure routes, target organs, LD50 values, human/non-human toxicity excerpts), and Ecological Information...
PubMed get article
Get complete metadata for a specific PubMed article by its PMID (PubMed ID) using efetch. Returns comprehensive article information including title, full abstract, complete author list with affiliations, journal details (name, volume, issue, pages), publication dates, DOI, MeSH terms, article type, grant information, and references. Essential for accessing full abstracts, detailed metadata, and citation information. Find PMIDs using PubMed_search_articles (format: integer like 12345678).
PubChemTox get toxicity values
Get non-human toxicity values (LD50, LC50, etc.) for a chemical compound from PubChem. Returns lethal dose/concentration data from animal studies, typically including LD50 (dose lethal to 50% of test animals) values for different species and routes of exposure. Data sourced from HSDB (Hazardous Substances Data Bank) and other toxicological databases. For example, aspirin (CID 2244) has LD50 values of 1800 mg/kg (rabbit, oral) and 1500 mg/kg (rat, oral). Arsenic (CID 5359596) has much lower LD...
PubMed get cited by
Get a list of PubMed articles that cite a specific PMID using elink. Returns PMIDs of articles that have cited the input article in their reference list. Use this to track citation impact, find more recent work building on a paper, or explore how research has been applied. Essential for literature reviews, impact analysis, and staying current with research developments. Find PMIDs using PubMed_search_articles.
PubMed get links
Get external links (LinkOut) for a specific PubMed article by its PMID using elink. Returns URLs to full-text providers, supplementary data, related resources, clinical trials, and other external content. Use this to access full-text articles, find supplementary materials, or discover related datasets and resources. Essential for accessing paywalled content via institutional subscriptions or finding open-access versions. Find PMIDs using PubMed_search_articles.
PubMed get related
Get related PubMed articles for a specific PMID using elink. Returns a list of computationally similar articles based on title, abstract, and MeSH terms. Use this to discover additional relevant literature, find similar studies, or explore a research topic more comprehensively. The algorithm identifies articles with similar content, methodology, or subject matter. Find PMIDs using PubMed_search_articles.
PubMed Guidelines Search
Search PubMed for peer-reviewed clinical practice guidelines using NCBI E-utilities. Filters results specifically for guideline and practice guideline publication types. Provides access to high-quality, evidence-based clinical guidelines from medical journals worldwide.
PubMed search articles
Search PubMed biomedical literature database using NCBI E-utilities (esearch + esummary). Returns articles with PMID, title, authors, journal, publication year, DOI, article type, and PubMed URL. Automatically fetches rich metadata for each article. Use this to discover medical/life sciences literature, find articles by topic, or search for publications by author or journal. Rate limiting is automatically handled (3 req/sec without API key, 10 req/sec with key set via NCBI_API_KEY environment...
QualityCheckerAgent
AI agent that checks search result quality and suggests improvements
reactome disease target score
Extract disease-target association scores from Reactome pathway data. This includes pathway-based evidence.
Reactome get complex
Get detailed information about a protein complex by its Stable ID. Returns comprehensive complex data including subunits, compartments, and related information. Uses the unified query endpoint that works for all entity types.
Reactome get database version
Get Reactome database version information. Returns version number as integer.
Reactome get entity compartment
Get compartment information for an entity. Returns TSV-formatted compartment data parsed into structured JSON. The API returns tab-separated values (ID, name, type) which are automatically converted to JSON format.
Reactome get diseases
Get list of disease pathways or DOIDs (Disease Ontology IDs) annotated in Reactome. Returns disease-related pathway information including database identifiers, definitions, and names.
Reactome get entity events
Get events (reactions/subpathways) associated with an entity. Returns TSV-formatted event data parsed into structured JSON. The API returns tab-separated values (ID, name, type) which are automatically converted to JSON format.
Reactome get event ancestors
Get ancestor events (parent pathways) for a reaction or pathway.
Reactome get events hierarchy
Get the full event hierarchy (pathways and reactions) for a specific species. Returns complete nested hierarchy structure with top-level pathways and their children (subpathways and reactions). Note: Use taxonomy ID (e.g., '9606') for best results.
Reactome get interactor
Get detailed information about an interactor (protein, complex, or small molecule) by its Stable ID. Returns comprehensive interactor data including reference entities, compartments, and related pathways. Uses the unified query endpoint that works for all entity types.
Reactome get participant reference entities
Get reference entities for participants of a reaction or event. Returns list of reference entities (UniProt proteins, ChEBI chemicals, etc.) associated with the participants, including database identifiers and names.
Reactome get participants
Get all participants (physical entities) of a reaction or event. Returns list of physical entities (proteins, complexes, small molecules) participating in the event, including their reference entities.
Reactome get pathway hierarchy
Get the hierarchy (parent pathways) for a pathway. Returns list of parent pathways.
Reactome get pathway reactions
Query all reactions and subpathways contained under a Pathway using Pathway Stable ID. Returns list of events (reactions and subpathways) contained in the pathway, including their metadata and relationships.
Reactome get pathway
Get detailed information about a specific pathway by its Stable ID. Returns comprehensive pathway data including metadata, compartments, literature references, orthologous events, and related pathways. Uses the unified query endpoint that works for all entity types.
Reactome get pathways low entity
Get low-level pathways (most specific pathways) containing a specific entity. Returns pathways at the lowest level of the hierarchy.
Reactome get reaction
Get detailed information about a specific reaction/event by its Stable ID. Returns comprehensive reaction data including inputs, outputs, regulation, literature references, and participants. Uses the unified query endpoint. Use Reactome_get_pathway_reactions to get valid reaction IDs first.
Reactome list species
List all species available in Reactome database.
Reactome list top pathways
List top-level pathways for a specific species. Returns pathways that have no parent pathways, including their metadata and basic information.
Reactome map uniprot to pathways
Map a UniProt protein identifier to Reactome pathways. Returns all pathways that contain this protein.
Reactome map uniprot to reactions
Map a UniProt protein identifier to Reactome reactions. Returns all reactions that involve this protein.
Reactome query by ids
Query Reactome by providing a list of Reactome stable identifiers (R-HSA-*). Returns detailed information about pathways, reactions, or other entities. Note: This endpoint requires Reactome stable IDs, not external IDs (UniProt, ChEBI). Use mapping endpoints first to convert external IDs to Reactome IDs.
RxNorm get drug names
Get RXCUI (RxNorm Concept Unique Identifier) and all associated names (generic names, brand names, synonyms, etc.) for a drug by its name. This tool uses the RxNorm API from the U.S. National Library of Medicine (NLM) to standardize drug names.
ResultSummarizerAgent
AI agent that summarizes search results for research plans
search clinical trials
Search ClinicalTrials.gov for clinical trials by disease/condition, drug/intervention, or keywords. This is the PRIMARY tool for finding clinical trials — use it when you need to discover trials for a drug (e.g., 'olaparib', 'pembrolizumab'), a disease (e.g., 'lung cancer', 'diabetes'), or any study criteria. Accepts condition names, intervention/treatment names, and free-text queries. Returns NCT IDs and brief descriptions with pagination. Use the returned NCT IDs with 'get_clinical_trial_*'...
SemanticScholar get pdf snippets
Fetch a paper's open-access PDF from Semantic Scholar and return bounded text snippets around provided terms. Uses markitdown to convert PDF to markdown. Useful when key details (methods, experimental parameters) are in the full text rather than abstract.
SemanticScholar search papers
Search for papers on Semantic Scholar including abstracts. This tool queries the Semantic Scholar API using natural language keywords and returns papers with details such as title, abstract, publication year, journal (venue), and URL. Rate limits: 1 req/sec without API key, 100 req/sec with SEMANTIC_SCHOLAR_API_KEY environment variable set.
SIDER get drug indications
Get the therapeutic indications for a drug from SIDER. Indications are medical conditions that a drug is approved to treat, extracted from the indications and usage sections of drug labels. Returns MedDRA-coded conditions with descriptions. Provide either a drug name or SIDER drug ID.
SIDER get drug side effects
Get the list of known side effects for a drug from SIDER, including frequency data when available. Side effects are extracted from drug labels and include MedDRA codes, frequency percentages from clinical trials (e.g., '21% - 57.5%'), and placebo comparison rates. Provide either a drug name (will auto-search) or a SIDER drug ID from SIDER_search_drug. Returns adverse reactions recorded in official drug labels.
SIDER get drugs for side effect
Find all drugs associated with a specific side effect in SIDER. Returns drugs known to cause the given adverse reaction, with frequency information when available (e.g., '7%', '5% - 18%', 'postmarketing', 'common'). Provide either a MedDRA code (e.g., C0018681 for headache) or a side effect name (will auto-search). Useful for drug safety comparisons and adverse event analysis.
SIDER search drug
Search the SIDER drug side effects database for a drug by name. Returns matching drugs with SIDER IDs and any related side effects. SIDER contains adverse drug reaction data extracted from drug labels for marketed medicines. Use this to find the SIDER drug ID needed for other SIDER operations (get_side_effects, get_indications).
SIDER search side effect
Search for a side effect by name in SIDER. Returns matching side effects with their MedDRA codes (UMLS CUIs). Use this to find the correct MedDRA code for a side effect before querying SIDER_get_drugs_for_side_effect. SIDER uses MedDRA (Medical Dictionary for Regulatory Activities) terminology for standardized adverse event reporting.
SIGN list guidelines
List all SIGN (Scottish Intercollegiate Guidelines Network) clinical guidelines, optionally filtered by clinical topic/specialty. Returns up to `limit` guidelines from the full SIGN table covering cardiovascular, oncology, mental health, and other specialties.
SIGN search guidelines
Search SIGN (Scottish Intercollegiate Guidelines Network) clinical guidelines by keyword. Fetches the complete SIGN guidelines table (84 evidence-based guidelines) and filters by keyword match in title or clinical topic. Returns guideline number, title, topic, publication year, and URL.
snomed search concepts
Search for SNOMED CT concepts using UMLS. Returns matching concepts with descriptions. Requires free UMLS API key (register at https://uts.nlm.nih.gov/uts/). Set UMLS_API_KEY environment variable.
SYNERGxDB get combo matrix
Get the dose-response matrix data for a specific drug combination experiment in SYNERGxDB. Returns concentration pairs and raw viability plus synergy matrices (Bliss, Loewe, HSA, ZIP). The combo_id and source_id can be obtained from SYNERGxDB_search_combos results.
SYNERGxDB get combo stats
Get per-dataset combination statistics from SYNERGxDB. Returns the number of unique drug combinations, total experiments, and data points for each screening study. Useful for understanding the scale and coverage of each integrated dataset.
SYNERGxDB get drug
Get detailed information about a specific drug in SYNERGxDB by its database ID. Returns drug name, ATC code, PubChem ID, and DrugBank ID. Known drug IDs: 11 (Bortezomib), 24 (Dasatinib), 34 (Erlotinib), 41 (Fluorouracil), 48 (Imatinib), 52 (Lapatinib), 97 (Topotecan), 106 (Vorinostat).
SYNERGxDB list cell lines
List all cancer cell lines in the SYNERGxDB database. Returns cell line names, tissue types, disease annotations, Cellosaurus IDs, and demographic data. Contains 151 cancer cell lines. Tissue types include blood, breast, lung, colon, CNS, ovary, prostate, kidney, skin.
SYNERGxDB list datasets
List all drug combination screening datasets integrated in SYNERGxDB. Returns dataset names, number of drugs, cell lines, and publication references. Key datasets: NCI-ALMANAC (101 drugs, 60 cell lines), MERCK (38 drugs, 39 cell lines), STANFORD, YALE-PDAC, YALE-TNBC, MIT-MELANOMA, CLOUD, ASTRAZENECA.
SYNERGxDB list drugs
List drugs in the SYNERGxDB database with their identifiers. Returns drug names, IDs, PubChem CIDs, DrugBank IDs, SMILES, InChIKey, and associated datasets. Contains 1977 unique compounds. Use 'query' or 'name' to filter by drug name (e.g., 'imatinib'). Use drug IDs from this list in SYNERGxDB_search_combos queries.
SYNERGxDB search combos
Search drug combination synergy scores in SYNERGxDB. Returns synergy metrics (Bliss, Loewe, HSA, ZIP) for drug pairs across cancer cell lines. Filter by drug IDs, cell line/tissue, and dataset. The database integrates 22,507 unique drug combinations from 9 major studies (NCI-ALMANAC, MERCK, MIT-MELANOMA, VISAGE, DECREASE, YALE-TNBC, YALE-PDAC, STANFORD, CLOUD). Positive ZIP scores indicate synergy. Use list_drugs first to find drug IDs. NOTE: SYNERGxDB covers pairwise in vitro cytotoxicity sc...
TCIA get body part values
Get the body parts examined in TCIA imaging collections. Returns body part names for filtering series queries. Optionally filter by collection or modality.
TCIA get modality values
Get the imaging modalities available in a specific TCIA collection or across all collections. Returns modality codes such as CT, MR, PT (PET), CR, DX, US (ultrasound), NM.
TCIA get patient studies
Get study information for patients in The Cancer Imaging Archive (TCIA). Returns study metadata including study date, description, and patient details. Filter by collection name or patient ID.
TCIA get series metadata
Get detailed DICOM metadata for a specific imaging series in TCIA by its Series Instance UID. Returns equipment information, acquisition parameters, and series attributes.
TCIA get series size
Get the total file size and image count for a specific imaging series in The Cancer Imaging Archive (TCIA). Returns total size in bytes and number of DICOM objects. Use this to estimate download sizes before retrieving imaging data. Obtain SeriesInstanceUID from TCIA_get_series results.
TCIA get series
Get imaging series from The Cancer Imaging Archive (TCIA). A series is a set of related images from a single imaging session. Returns metadata including modality, body part, patient ID, image count, and file size. Filter by collection name, patient ID, study UID, modality, or body part. Example collections: 'TCGA-GBM', 'LIDC-IDRI', 'TCGA-LUAD', 'TCGA-BRCA'.
TCIA list collections
List all publicly available imaging collections in The Cancer Imaging Archive (TCIA). TCIA is a large archive of medical images of cancer available for public download. Returns collection names for use with other TCIA tools.
TRIP Database Guidelines Search
Search TRIP Database (Turning Research into Practice) for evidence-based clinical guidelines. TRIP is a specialized clinical search engine that focuses on high-quality evidence-based content, particularly clinical guidelines from reputable sources worldwide.
umls get concept details
Get detailed information about a UMLS concept by its CUI (Concept Unique Identifier). Returns concept details, atoms, definitions, relations, and mappings to other terminologies. Requires free UMLS API key (register at https://uts.nlm.nih.gov/uts/). Set UMLS_API_KEY environment variable.
umls search concepts
Search for concepts in UMLS (Unified Medical Language System) using concept names or terms. UMLS provides access to multiple medical terminologies including SNOMED CT, ICD-10, ICD-11, LOINC, RxNorm, and more. Requires free UMLS API key (register at https://uts.nlm.nih.gov/uts/). Set UMLS_API_KEY environment variable.
WHO Guideline Full Text
Fetch full text content from a WHO (World Health Organization) guideline publication page. Extracts available web content and finds PDF download links. Use this after finding a guideline with WHO_Guidelines_Search to get the full content or PDF link.
WHOGHO get indicator data
Get actual health data values for a specific WHO Global Health Observatory indicator by its code. Returns country-level data with values, confidence intervals, year, and sex/age breakdowns. No authentication required. Common indicator codes: WHOSIS_000001 (life expectancy at birth), MALARIA002 (malaria cases), MDG_0000000026 (HIV prevalence), NCD_BMI_30C (obesity prevalence), SDGPM25 (PM2.5 air pollution), WHS4_100 (hospital beds per 10000).
WHO Guidelines Search
Search WHO (World Health Organization) official clinical guidelines and health recommendations. Provides access to authoritative global health guidelines published by WHO.
WHOGHO search indicators
Search WHO Global Health Observatory (GHO) health indicators by name using the ODATA API. Returns indicator codes and names covering mortality, disease, nutrition, maternal health, mental health, and more. No authentication required. Use indicator codes with WHOGHO_get_indicator_data to retrieve actual data values. Examples: 'life expectancy' (WHOSIS_000001), 'malaria' (MALARIA002), 'obesity' (NCD_BMI_30C).
Medical Board Exam Preparation
USMLE/COMLEX board exam preparation tool with practice questions, spaced repetition, and high-yield topic reviews. Tracks performance and identifies weak areas.
ACLS Protocol Assistant
Advanced Cardiac Life Support (ACLS) protocol guide for emergency resuscitation. Provides step-by-step guidance for cardiac arrest, arrhythmia management, and post-cardiac arrest care.
CBT Therapeutic Techniques Guide
Evidence-based cognitive behavioral therapy (CBT) tools and worksheets. Includes thought records, behavioral activation, and cognitive restructuring exercises.
Developmental Milestone Tracker
Track and assess pediatric developmental milestones from birth to 5 years. Flags potential delays using CDC developmental surveillance guidelines.
GAD-7 Anxiety Screening Tool
Generalized Anxiety Disorder 7-item (GAD-7) screening tool with automated scoring. Assesses anxiety severity and guides treatment decisions.
Interactive Anatomy Learning Assistant
Interactive anatomy education tool with 3D anatomical references, clinical correlations, and self-assessment questions. Covers all major organ systems.
Clinical Case Scenario Generator
Generate realistic clinical case scenarios for medical education and assessment. Customizable by specialty, complexity level, and learning objectives.
Nursing Care Plan Generator
Generate evidence-based nursing care plans with NANDA-I diagnoses, NOC outcomes, and NIC interventions. Supports individualized patient care planning.
Outbreak Investigation Assistant
Systematic approach to outbreak investigation using CDC guidelines. Assists with case definition, epidemic curve analysis, and source identification.
Nursing Patient Assessment Tool
Comprehensive nursing assessment tool for systematic patient evaluation. Covers vital signs interpretation, pain assessment, fall risk screening, and activities of daily living.
Pediatric Drug Dosing Calculator
Weight-based and body-surface-area-based drug dosing calculator for pediatric patients. Includes common pediatric medications with age-appropriate dosing ranges.
PHQ-9 Depression Screening Tool
Validated Patient Health Questionnaire-9 (PHQ-9) for depression screening and severity assessment. Automatic scoring and interpretation with suicide risk flagging.
Immunization Schedule Tracker
CDC/WHO immunization schedule tracker for pediatric and adult vaccinations. Identifies overdue vaccines and generates catch-up schedules.
WHO Surgical Safety Checklist
Digital implementation of the WHO Surgical Safety Checklist for pre-operative, intra-operative, and post-operative verification. Reduces surgical complications and improves team communication.
Trauma Management Protocols (ATLS)
Advanced Trauma Life Support (ATLS) protocol assistant for initial assessment and management of trauma patients. Covers primary/secondary surveys and critical interventions.
Biostatistics Analysis Tool
Perform common biostatistical analyses for medical research including survival analysis, logistic regression, ROC curves, and sample size calculations.
Clinical Differential Diagnosis Assistant
AI-powered clinical decision support tool that helps generate comprehensive differential diagnoses based on patient symptoms, lab results, and medical history. Integrates evidence-based clinical reasoning and medical literature.
Clinical Practice Guideline Navigator
Search and navigate clinical practice guidelines from major organizations (AHA, ACC, ACP, IDSA, etc.). Provides evidence-graded recommendations for common clinical scenarios.
Clinical Treatment Plan Generator
Generate comprehensive clinical treatment plans with SMART goal frameworks and evidence-based interventions. Exports to LaTeX/PDF format for clinical documentation.
ClinicalTrials.gov Database Access
Access 400,000+ clinical trials from 220+ countries via ClinicalTrials.gov API v2. Search by condition, intervention, sponsor, or location.
CPT Procedure Code Assistant
AI-driven CPT coding validation and suggestion tool. Validates procedure codes against clinical documentation and identifies potential coding gaps.
DICOM Metadata & PHI Anonymization
Extract metadata from DICOM medical images, anonymize protected health information (PHI), and process imaging data for research or clinical workflows. Supports pydicom integration.
Drug Interaction Safety Checker
Real-time drug-drug interaction detection with five-level severity classification (A/B/C/D/X). Checks for drug-disease, drug-dose, and drug-food interactions using FDA and clinical databases.
DrugBank Comprehensive Drug Database
Access 17,430+ drugs (13,166 small molecules + 4,264 biotech drugs) with high-performance SQLite backend. Search by name, therapeutic category, elimination half-life, or molecular similarity.
Epidemiology & Disease Surveillance
Access WHO Global Health Observatory data for epidemiological analysis. Track disease prevalence, mortality rates, and public health indicators by country and region.
Emergency Department Triage Protocols
AI-assisted emergency department triage tool with evidence-based protocols for rapid patient assessment. Helps prioritize cases based on acuity and clinical presentation.
Clinical Evidence Synthesis Tool
Synthesizes clinical evidence from multiple sources including PubMed, Cochrane, and clinical guidelines. Generates evidence summaries with quality grading.
FDA Drug Information & Adverse Events
Access comprehensive FDA drug databases including adverse events (FAERS), drug labels, NDC directory, recalls, shortages, and 510(k) device clearances via openFDA API.
FHIR Healthcare Data Access
Connect to FHIR-compliant electronic health record systems to query, retrieve, and analyze patient data using natural language. Supports full CRUD operations on FHIR resources with SMART-on-FHIR authentication.
FDA 510(k) Documentation Automation
Automates FDA-required documentation for Software as a Medical Device (SaMD) including 510(k) submissions. Generates traceability matrices linking code to regulatory requirements.
Genomic Variant Interpretation
Interpret genomic variants using ClinVar, gnomAD, and other genomic databases. Provides pathogenicity classification and clinical significance assessment.
HIPAA Compliance & De-identification
Clinical de-identification pipeline that detects 30+ PHI entity types. Provides masked and obfuscated output modes for HIPAA compliance. Runs locally with data never leaving secure environment.
ICD-10 Diagnosis Code Lookup
Search and validate ICD-10-CM diagnosis codes using NLM Clinical Tables API. Supports partial matching and hierarchical browsing of code categories.
IEC 62304 Medical Device Software Lifecycle
Modular skills for AI coding agents working on medical device software. Aligned to IEC 62304, ISO 14971, FDA, and EU MDR standards for software lifecycle management.
Lab Result Interpretation Assistant
Automatically extract and interpret biochemical test data from lab reports. Provides clinical significance analysis, reference range comparisons, and flags critical values.
Medical Imaging & DICOM Analysis
Analyze medical imaging data from DICOM servers and PACS systems. Extract metadata, query imaging studies by patient or modality, and process diagnostic imaging reports for clinical decision support.
Medical Academic Writing Humanizer
Removes signs of AI-generated writing from medical papers and makes them sound more natural. Based on Wikipedia's AI writing guide, adapted for medical literature.
Medicare Drug Spending & Utilization
Access CMS Medicare data including physician services, prescriber data, hospital utilization, and drug spending analysis via Socrata API.
Medication Administration Safety Check
Five Rights of medication administration checker for nursing. Verifies right patient, drug, dose, route, and time before medication administration.
Pediatric Growth Chart Analyzer
Interpret pediatric growth measurements using CDC and WHO growth charts. Plots height, weight, BMI, and head circumference percentiles for age and gender.
Precision Medicine Treatment Planning
Generate personalized treatment plans based on pharmacogenomics, variant interpretation, and patient-specific data. Integrates ClinPGx and ClinVar databases for evidence-based precision therapeutics.
Prior Authorization Review Assistant
Official Anthropic skill for insurance prior authorization review workflows. Cross-references coverage requirements, clinical guidelines, and patient records.
Protein Structure Database (AlphaFold & PDB)
Access AlphaFold Protein Structure Database and Protein Data Bank (PDB) for structural biology research. Analyze protein structures and molecular interactions.
Medical Radiation Exposure Tracker
Track cumulative radiation exposure from medical imaging procedures (X-rays, CT scans). Includes body surface area adjustments and radioactive decay models for comprehensive dosimetry.
RAF Score & HCC Calculator
Risk Adjustment Factor (RAF) score calculator with Hierarchical Condition Category (HCC) capture from encounter documentation for Medicare Advantage.
PubMed Medical Literature Search
Search 36M+ citations from PubMed and PubMed Central. Advanced search with boolean operators, MeSH terms, author/journal filters, and full-text access.
Supplement-Drug Interaction Safety
First supplement-drug interaction safety tool for AI agents. Evidence-based supplement safety intelligence with 805 FDA FAERS adverse event signals and CYP450 pathway analysis.
Systematic Review & Meta-Analysis Assistant
Assists with systematic review methodology including PICO formulation, search strategy development, study selection, and quality assessment using PRISMA guidelines.
Surgical Procedure Planning Assistant
Pre-operative planning tool for surgical procedures. Assists with procedure selection, anatomical considerations, equipment checklists, and patient positioning protocols.