Search PubMed biomedical literature by keyword, author, or MeSH term (e.g., "cancer immunotherapy", "author:Smith J"). Returns PubMed IDs for fetching full details.
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130,895 tools. Last updated 2026-05-07 18:16
"PubMed Biomedical Literature Search" matching MCP tools:
- Search PubMed biomedical literature by natural language query. Examples: 'SGLT2 inhibitors heart failure outcomes 2022', 'mRNA vaccine immunogenicity elderly', 'GLP-1 agonist weight loss meta-analysis'Connector
- Search PubMed biomedical literature by natural language query. Examples: 'SGLT2 inhibitors heart failure outcomes 2022', 'mRNA vaccine immunogenicity elderly', 'GLP-1 agonist weight loss meta-analysis'Connector
- Search Cochrane systematic reviews via PubMed. Finds Cochrane Database of Systematic Reviews articles matching your query. Returns PubMed IDs, titles, and publication dates. Use get_review_detail with a PMID to get the full abstract. Args: query: Search terms for finding reviews (e.g. 'diabetes exercise', 'hypertension treatment', 'childhood vaccination safety'). limit: Maximum number of results to return (default 20, max 100).Connector
- Map identifiers between databases. SYNTAX: biobtree_map(terms="ID", chain=">>source>>target") - Chain MUST start with ">>" - Source MUST match input ID type ID TYPE → SOURCE: - ENSG* → >>ensembl - P*/Q*/O* → >>uniprot - CHEMBL* → >>chembl_molecule - GO:* → >>go - MONDO:* → >>mondo - HP:* → >>hpo - HGNC:* or gene symbols → >>hgnc SOME DRUG EXPLORATION PATHS: - >>chembl_molecule>>chembl_target>>uniprot (drug targets) - >>pubchem>>pubchem_activity>>uniprot (bioactivity) - >>gtopdb_ligand>>gtopdb_interaction>>gtopdb>>uniprot (curated pharmacology with affinity data) - >>ensembl>>reactome>>chebi (pathway chemicals - when no direct targets) - Discover more via entry xrefs + EDGES WARNING - GO terms with high xref_count (>100): - Don't map GO → proteins → drugs (too many results) - Instead: search drug class for condition → verify targets this GO term DISEASE GENE PATTERNS: - >>mondo>>gencc>>hgnc (curated) - >>mondo>>clinvar>>hgnc (variant-based) DISEASE → DRUG PATTERNS: - >>mesh>>chembl_molecule (MeSH disease/condition → drugs with indications) - >>mondo>>clinical_trials>>chembl_molecule (disease → trial drugs) DISCOVERY APPROACH: - Use biobtree_entry to see xrefs (what's connected) - Use EDGES above to see where each dataset leads - Build chains based on what connections exist for YOUR entity RETURNS: mapped identifiers with dataset and name EDGES (what connects to what): ensembl: uniprot, go, transcript, exon, ortholog, paralog, hgnc, entrez, refseq, bgee, gwas, gencc, antibody, scxa hgnc: ensembl, uniprot, entrez, gencc, pharmgkb_gene, msigdb, clinvar, mim, refseq, alphafold, collectri, gwas, dbsnp, hpo, cellphonedb entrez: ensembl, uniprot, refseq, go, biogrid, pubchem_activity, ctd_gene_interaction refseq: ensembl, entrez, taxonomy, ccds, uniprot, mirdb mirdb: refseq transcript: ensembl, exon, ufeature uniprot: ensembl, alphafold, interpro, pfam, pdb, ufeature, intact, string, string_interaction, biogrid, biogrid_interaction, chembl_target, go, reactome, rhea, swisslipids, bindingdb, antibody, pubchem_activity, cellphonedb, jaspar, signor, diamond_similarity, esm2_similarity alphafold: uniprot interpro: uniprot, go, interproparent, interprochild chembl_molecule: mesh, chembl_activity, chembl_target, pubchem, chebi, clinical_trials chembl_activity: chembl_molecule, chembl_assay, bao chembl_assay: chembl_activity, chembl_target, chembl_document, bao chembl_target: chembl_assay, uniprot, chembl_molecule pubchem: chembl_molecule, chebi, hmdb, pubchem_activity, pubmed, patent_compound, bindingdb, ctd, pharmgkb pubchem_activity: pubchem, ensembl, uniprot chebi: pubchem, rhea, intact swisslipids: uniprot, go, chebi, uberon, cl lipidmaps: chebi, pubchem dbsnp: hgnc, clinvar, pharmgkb_variant, alphamissense, spliceai clinvar: hgnc, mondo, hpo, dbsnp, orphanet alphamissense: uniprot, transcript gwas: gwas_study, efo, dbsnp, hgnc, mondo gwas_study: gwas, efo, mondo mondo: gencc, clinvar, efo, mesh, hpo, clinical_trials, antibody, cellxgene, cellxgene_celltype, orphanet, mondoparent, mondochild, gwas, gwas_study gencc: mondo, hpo, hgnc, ensembl clinical_trials: mondo, chembl_molecule pharmgkb: hgnc, dbsnp, mesh, pharmgkb_gene, pharmgkb_variant, pharmgkb_clinical, pharmgkb_guideline, pharmgkb_pathway pharmgkb_variant: pharmgkb_clinical, hgnc, mesh, dbsnp pharmgkb_gene: hgnc, entrez, ensembl, pharmgkb pharmgkb_clinical: dbsnp, hgnc, mesh, pharmgkb_variant pharmgkb_guideline: hgnc, pharmgkb pharmgkb_pathway: hgnc, pharmgkb ctd: mesh, ctd_gene_interaction, ctd_disease_association, pubchem ctd_gene_interaction: ctd, entrez, taxonomy, pubmed ctd_disease_association: ctd, mesh, mim, pubmed intact: uniprot, chebi, rnacentral string: uniprot, string_interaction string_interaction: string, uniprot biogrid: entrez, uniprot, refseq, taxonomy bgee: ensembl, uberon, cl, taxonomy, bgee_evidence bgee_evidence: bgee, uberon, cl cellxgene: cl, uberon, mondo, efo, taxonomy cellxgene_celltype: cl, uberon, mondo scxa: cl, uberon, taxonomy, ensembl, scxa_gene_experiment scxa_expression: ensembl, scxa, scxa_gene_experiment scxa_gene_experiment: ensembl, scxa, scxa_expression, cl rnacentral: uniprot, ensembl, intact, hgnc, refseq, ena reactome: ensembl, uniprot, chebi, go, reactomeparent, reactomechild rhea: chebi, uniprot, go go: ensembl, uniprot, reactome, msigdb, swisslipids, bgee, interpro, goparent, gochild hpo: clinvar, gencc, mondo, msigdb, orphanet, mim, hmdb, hgnc, hpoparent, hpochild efo: gwas, mondo, cellxgene, efoparent, efochild uberon: bgee, cellxgene, cellxgene_celltype, swisslipids, uberonparent, uberonchild cl: bgee, cellxgene, cellxgene_celltype, scxa, scxa_gene_experiment, clparent, clchild taxonomy: ensembl, uniprot, bgee, biogrid, ctd_gene_interaction, taxparent, taxchild mesh: pharmgkb, ctd, ctd_disease_association, pubchem, mondo, chembl_molecule, meshparent, meshchild eco: ecoparent, ecochild antibody: ensembl, uniprot, mondo, pdb msigdb: hgnc, entrez, go, hpo orphanet: hpo, uniprot, mondo, hgnc, clinvar, mim, mesh mim: clinvar, hpo, mondo, uniprot, ctd_disease_association hmdb: pubchem, hpo, chebi, uniprot collectri: hgnc # transcription factor → target gene interactions esm2_similarity: uniprot # protein structural similarity diamond_similarity: uniprot # protein sequence similarity cellphonedb: uniprot, ensembl, hgnc, pubmed # ligand-receptor pairs for cell-cell communication spliceai: hgnc pdb: uniprot, go, interpro, pfam, taxonomy, pubmed fantom5_promoter: ensembl, hgnc, entrez, uniprot, uberon, cl fantom5_enhancer: ensembl, uberon, cl fantom5_gene: ensembl, hgnc, entrez jaspar: uniprot, pubmed, taxonomy encode_ccre: taxonomy bao: chembl_activity, chembl_assay, baoparent, baochild brenda: uniprot, pubmed, brenda_kinetics, brenda_inhibitor brenda_kinetics: brenda brenda_inhibitor: brenda gtopdb: uniprot, hgnc, gtopdb_ligand, gtopdb_interaction # drug targets (GPCRs, ion channels, enzymes) gtopdb_ligand: pubchem, chebi, chembl_molecule, gtopdb_interaction # ligands/drugs with binding data gtopdb_interaction: gtopdb, gtopdb_ligand, pubmed # target-ligand binding with affinity values FILTER SYNTAX: >>dataset[field operator value] OPERATORS: == equals >>dataset[field=="value"] != not equals >>dataset[field!="value"] > greater than >>dataset[field>value] < less than >>dataset[field<value] >= greater or equal >>dataset[field>=value] <= less or equal >>dataset[field<=value] contains string match >>dataset[field.contains("value")] LOGICAL OPERATORS: && AND >>dataset[field1>5 && field2<10] || OR >>dataset[field=="A" || field=="B"] ! NOT >>dataset[!field] or >>dataset[!(field=="value")] TYPE RULES: - FLOAT: use decimal point (70.0 not 70) - INT: no decimal (2 not 2.0) - STRING: quote values ("Pathogenic", "PHASE3") - BOOL: true/false (no quotes) EXAMPLES: >>chembl_molecule[highestDevelopmentPhase==4] # approved drugs >>chembl_molecule[highestDevelopmentPhase>=3] # Phase 3+ >>clinical_trials[phase=="PHASE3"] >>go[type=="biological_process"] >>clinvar[germline_classification=="Pathogenic"] >>reactome[name.contains("signaling")] >>gtopdb[type=="gpcr"] # GPCR targets >>gtopdb[type=="ion_channel"] # ion channel targets >>gtopdb_ligand[approved==true] # approved drugs only >>gtopdb_interaction[endogenous==true] # endogenous ligand interactionsConnector
- Search 646+ skills using TF-IDF semantic search. Returns ranked skills with scores. Use this to discover capabilities before calling execute_skill.Connector
Matching MCP Servers
- AlicenseAqualityCmaintenanceAn MCP server that provides direct access to PubMed and PubMed Central via the NCBI E-utilities API. It enables AI models to search biomedical literature, retrieve detailed article metadata, and download open-access full texts.Last updated5MIT
- AlicenseAqualityCmaintenanceAn MCP server that provides access to PubMed and NCBI's biomedical literature database for searching articles, retrieving metadata, and tracking citations. It enables users to explore related research, browse MeSH vocabulary, and find free full-text links.Last updated326MIT
Matching MCP Connectors
Search biomedical literature, get article details, find related articles, and explore MeSH terms
Search 36M+ PubMed biomedical articles and ClinicalTrials.gov studies.
- Search current promotions (Aktionen) across all 22 Swiss retailers. Uses full-text search + trigram matching directly on the deals database. Free — does not consume search credits. Returns product name, price, original price, discount %, retailer, category, and validity dates.Connector
- Search the MeSH vocabulary for standardized medical terms. Find MeSH (Medical Subject Headings) descriptors to use in precise PubMed searches. Returns MeSH IDs, preferred terms, and scope notes. Args: term: Search term (e.g. 'diabetes', 'heart failure', 'opioid'). limit: Maximum results (default 10).Connector
- Get the full abstract and metadata of an MMWR article by PubMed ID. Returns the complete abstract, authors, publication date, volume/issue, and any MeSH subject headings. Use PMIDs from search_mmwr or get_recent_reports results. Args: pmid: PubMed ID of the MMWR article (e.g. '38271059').Connector
- Find the planning portal URL for a UK postcode. Returns council info and portal search URLs. Does not scrape planning applications -- use the returned URLs to search directly.Connector
- Edit a file in the solution's GitHub repo and commit. Two modes: 1. FULL FILE: provide `content` — replaces entire file (good for new files or small files) 2. SEARCH/REPLACE: provide `search` + `replace` — surgical edit without sending full file (preferred for large files like server.js) Always use search/replace for large files (>5KB). Always read the file first with ateam_github_read to get the exact text to search for.Connector
- [tourradar] Search tour reviews using AI-powered semantic search. Requires tourIds to scope results to specific tours. Use this when the user asks about reviews, feedback, or experiences for specific tours. Combine with an optional text query to find reviews mentioning specific topics (e.g., 'food', 'guide', 'accommodation'). When you don't have tour IDs, use vertex-tour-search or vertex-tour-title-search first to find them.Connector
- POST /v1/contact/search. Search for contacts at specified companies. Returns a job_id (async, 202). enrich_fields required (at least one of contact.emails or contact.phones). Use company_list (slug) instead of domains to search a saved list.Connector
- Estimate the credit cost of an analysis before running it. Returns credit cost, whether you have sufficient credits, and whether a free public alternative exists. Always call this before discovery_analyze for private runs. Args: file_size_mb: Size of the dataset in megabytes. num_columns: Number of columns in the dataset. analysis_depth: Search depth (1=fast, higher=deeper). Default 1. visibility: "public" (free, results published) or "private" (costs credits). use_llms: Slower and more expensive, but you get smarter pre-processing, summary page, literature context and pattern novelty assessment. Only applies to private runs — public runs always use LLMs. Default false. api_key: Disco API key (disco_...). Optional if DISCOVERY_API_KEY env var is set.Connector
- Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.Connector
- Search 6,940 Harmonized System tariff codes. HS codes are 6-digit international product classification codes used for customs. Provide a search term or exact code.Connector
- Search the web via Brave Search API with local QVAC LLM cleaning. Returns cleaned markdown summaries. Use for general web research, factual lookups, and topic exploration.Connector
- Search a company's knowledge base for policies, procedures, and documentation. First use lookup_company to get the tenant_id, then use this tool to search their knowledge base.Connector
- Search user memories by keyword, type, tags, or date range. With query: Case-insensitive keyword search on content. Without query: Returns memories by recency. Use type filter to search only facts or only moments.Connector
- Deprecated — use `search` with `type: ['orgs', 'catalog']` instead. Semantic search across the registry returning orgs, products, or sources that match the query by meaning, not just keyword. Falls back to LIKE-based lexical search when Vectorize is unavailable.Connector