BioMCP

This tool retrieves full information for articles, clinical trials, genetic variants, genes, drugs, or diseases using their unique identifiers. It returns data in a standardized format suitable for detailed analysis and research. ## IDENTIFIER FORMATS: - Articles: PMID (PubMed ID) - e.g., "35271234" OR DOI - e.g., "10.1101/2024.01.20.23288905" - Trials: NCT ID (ClinicalTrials.gov ID) - e.g., "NCT04280705" - Variants: HGVS notation or dbSNP ID - e.g., "chr7:g.140453136A>T" or "rs121913254" - Genes: Gene symbol or Entrez ID - e.g., "BRAF" or "673" - Drugs: Drug name or ID - e.g., "imatinib" or "DB00619" - Diseases: Disease name or ID - e.g., "melanoma" or "MONDO:0005105" - NCI Organizations: NCI organization ID - e.g., "NCI-2011-03337" - NCI Interventions: NCI intervention ID - e.g., "INT123456" - NCI Diseases: NCI disease ID - e.g., "C4872" The domain is automatically detected from the ID format if not provided: - NCT* → trial - Contains "/" with numeric prefix (DOI) → article - Pure numeric → article (PMID) - rs* or contains ':' or 'g.' → variant - For genes, drugs, diseases: manual specification recommended ## DOMAIN-SPECIFIC OPTIONS: ### Articles (domain="article"): - Returns full article metadata, abstract, and full text when available - Supports both PubMed articles (via PMID) and Europe PMC preprints (via DOI) - Includes annotations for genes, diseases, chemicals, and variants (PubMed only) - detail="full" attempts to retrieve full text content (PubMed only) ### Clinical Trials (domain="trial"): - detail=None or "protocol": Core study information - detail="locations": Study sites and contact information - detail="outcomes": Primary/secondary outcomes and results - detail="references": Related publications and citations - detail="all": Complete trial record with all sections ### Variants (domain="variant"): - Returns comprehensive variant information including: - Clinical significance and interpretations - Population frequencies - Gene/protein effects - External database links - detail parameter is ignored (always returns full data) ### Genes (domain="gene"): - Returns gene information from MyGene.info including: - Gene symbol, name, and type - Entrez ID and Ensembl IDs - Gene summary and aliases - RefSeq information - detail parameter is ignored (always returns full data) ### Drugs (domain="drug"): - Returns drug/chemical information from MyChem.info including: - Drug name and trade names - Chemical formula and structure IDs - Clinical indications - Mechanism of action - External database links (DrugBank, PubChem, ChEMBL) - detail parameter is ignored (always returns full data) ### Diseases (domain="disease"): - Returns disease information from MyDisease.info including: - Disease name and definition - MONDO ontology ID - Disease synonyms - Cross-references to other databases - Associated phenotypes - detail parameter is ignored (always returns full data) ### NCI Organizations (domain="nci_organization"): - Returns organization information from NCI database including: - Organization name and type - Full address and contact information - Research focus areas - Associated clinical trials - Requires NCI API key - detail parameter is ignored (always returns full data) ### NCI Interventions (domain="nci_intervention"): - Returns intervention information from NCI database including: - Intervention name and type - Synonyms and alternative names - Mechanism of action (for drugs) - FDA approval status - Associated clinical trials - Requires NCI API key - detail parameter is ignored (always returns full data) ### NCI Diseases (domain="nci_disease"): - Returns disease information from NCI controlled vocabulary including: - Preferred disease name - Disease category and classification - All known synonyms - Cross-reference codes (ICD, SNOMED) - Requires NCI API key - detail parameter is ignored (always returns full data) ## RETURN FORMAT: All fetch operations return a standardized format: ```json { "id": "unique_identifier", "title": "Record title or name", "text": "Full content or comprehensive description", "url": "Link to original source", "metadata": { // Domain-specific additional fields } } ``` ## EXAMPLES: Fetch article by PMID (domain auto-detected): ``` await fetch(id="35271234") ``` Fetch article by DOI (domain auto-detected): ``` await fetch(id="10.1101/2024.01.20.23288905") ``` Fetch complete trial information (domain auto-detected): ``` await fetch( id="NCT04280705", detail="all" ) ``` Fetch variant with clinical interpretations: ``` await fetch(id="rs121913254") ``` Explicitly specify domain (optional): ``` await fetch( domain="variant", id="chr7:g.140453136A>T" ) ```

{ "properties": { "api_key": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "NCI API key for fetching NCI records (nci_organization, nci_intervention, nci_disease). Required for NCI fetches. Get a free key at: https://clinicaltrialsapi.cancer.gov/", "title": "Api Key" }, "call_benefit": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Brief explanation of why this fetch is being performed and expected benefit. Helps provide context for analytics and improves result relevance.", "title": "Call Benefit" }, "detail": { "anyOf": [ { "enum": [ "protocol", "locations", "outcomes", "references", "all", "full" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Detail" }, "domain": { "anyOf": [ { "enum": [ "article", "trial", "variant", "gene", "drug", "disease", "nci_organization", "nci_intervention", "nci_biomarker", "nci_disease", "fda_adverse", "fda_label", "fda_device", "fda_approval", "fda_recall", "fda_shortage" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "Domain of the record (auto-detected if not provided)", "title": "Domain" }, "id": { "title": "Id", "type": "string" } }, "required": [ "id" ], "title": "fetchArguments", "type": "object" }