"PubMed Biomedical Literature Search" matching MCP tools:

• search_biomedical_literatureA

  Noodle Biomedical Literature Discovery MCPA

  Semantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.

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• search_pubmedA

  PubMed / MEDLINE Literature SearchA

  Search PubMed for biomedical literature. Find research articles, reviews, and clinical studies matching your search terms. Supports PubMed query syntax including MeSH terms, field tags, and boolean operators. Args: query: Search terms (e.g. 'diabetes prevention exercise', 'breast cancer[MeSH] AND immunotherapy', 'COVID-19 vaccine efficacy'). limit: Maximum results (default 20, max 100). sort: Sort order - 'relevance', 'date', or 'author' (default 'relevance').

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• search_pubmedA

  tollboothC

  Search 37M+ biomedical papers via NCBI PubMed. PMIDs, titles, authors, journals.

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• search_pubmedA

  The Mine WorksA

  Search PubMed for biomedical literature. Returns PMID, title, abstract, authors, journal, and DOI. 36M+ articles indexed.

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• search_pubmedB

  Academic Research SearchA

  Search PubMed biomedical literature database (NIH). Returns articles with titles, authors, journals, and links.

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• discovery_estimateA

  DiscoA

  Estimate the credits required to run a Disco analysis. Returns `required_credits` for public (always 0) and private, with private split by whether LLMs are enabled (use_llms=False is faster, use_llms=True adds smarter preprocessing, literature context and a written summary). Also returns per-visibility depth caps and accepted file formats. No authentication required — when an API key is supplied, also returns the caller's available credits. Call this before discovery_analyze whenever cost or feasibility is unclear. 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). Used to compute the private-run cost. Default 2. api_key: Disco API key (disco_...). Optional. When provided, the response includes `account.available_credits`.

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• discovery_analyzeA

  DiscoA

  Run Disco on tabular data to find novel, statistically validated patterns. This is NOT another data analyst — it's a discovery pipeline that systematically searches for feature interactions, subgroup effects, and conditional relationships nobody thought to look for, then validates each on hold-out data with FDR-corrected p-values and checks novelty against academic literature. This is a long-running operation. Returns a run_id immediately. Use discovery_status to poll and discovery_get_results to fetch completed results. Use this when you need to go beyond answering questions about data and start finding things nobody thought to ask. Do NOT use this for summary statistics, visualization, or SQL queries. Public runs are free but results are published. Private runs cost credits. Call discovery_estimate first to check cost. Private report URLs require sign-in — tell the user to sign in at the dashboard with the same email address used to create the account (email code, no password needed). Call discovery_upload first to upload your file, then pass the returned file_ref here. Args: target_column: The column to analyze — what drives it, beyond what's obvious. file_ref: The file reference returned by discovery_upload. analysis_depth: Search depth (1=fast, higher=deeper). Default 1. visibility: "public" (free) or "private" (costs credits). Default "public". title: Optional title for the analysis. description: Optional description of the dataset. excluded_columns: Optional JSON array of column names to exclude from analysis. column_descriptions: Optional JSON object mapping column names to descriptions. Significantly improves pattern explanations — always provide if column names are non-obvious (e.g. {"col_7": "patient age", "feat_a": "blood pressure"}). author: Optional author name for the report. source_url: Optional source URL for the dataset. 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.

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  Destructive

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• biobtree_mapA

  BioBTreeA

  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) - >>hgnc>>clingen_gene_validity (ClinGen evidence tier), >>hgnc>>clingen_dosage (haploinsufficiency), >>hgnc>>clingen_variant>>clinvar (ACMG, then dbsnp) CANCER / CELL LINE: - >>hgnc>>intogen (cancer driver gene?), >>hgnc>>civic (clinical variant interpretations) - >>uniprot>>cellosaurus (cell lines for a protein/gene) - >>hgnc>>depmap (CRISPR essentiality / target tractability), >>hgnc>>entrez>>depmap_dependency>>cellosaurus (which lines depend on the gene) GENE FUNCTION / LITERATURE: - >>entrez>>generif (cited one-line functional claims; >>generif>>pubmed for citations) 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, civic, intogen, hpa, hpa_antibody, pharmgkb_var_annotation, chembl_mechanism, ncrna_disease, ncrna_interaction, ncrna_drug, alliance_disease, gnomad_constraint, drugcentral, panelapp_gene hgnc: ensembl, uniprot, entrez, gencc, pharmgkb_gene, msigdb, clinvar, mim, refseq, alphafold, collectri, gwas, hpo, cellphonedb, civic, intogen, cellosaurus, clingen_gene_validity, clingen_dosage, clingen_variant, depmap, hpa, pharmgkb_var_annotation, chembl_mechanism, ncrna_disease, ncrna_interaction, ncrna_drug, alliance_disease, drugcentral, panelapp_gene, gnomad_constraint, mavedb entrez: ensembl, uniprot, refseq, go, biogrid, pubchem_activity, ctd_gene_interaction, dbsnp, civic, intogen, clingen_dosage, generif, depmap, depmap_dependency, hpa, pharmgkb_var_annotation, orthologentrez, relatedentrez, neighborentrez, mgi, rgd, zfin, wormbase, xenbase, sgd, flybase, gnomad_constraint, drugcentral orthologentrez: entrez # cross-species gene orthologs (NCBI gene_orthologs). >>entrez>>orthologentrez gives ortholog genes (filter species via taxonomy); reliable from model-organism genes (human-gene side currently incomplete) relatedentrez: entrez # related genes (bidirectional): NCBI gene_group (functional gene/pseudogene/readthrough/region) + HGNC gene-family co-members neighborentrez: entrez # genomic neighbors (left/right/overlapping); edge carries distance + side, neighbor strand/position in attrs; filter to genes via [type!="biological-region"] gnomad_constraint: ensembl, entrez, hgnc, transcript # gene LoF constraint (pLI/LOEUF/oe_lof); reach via >>ensembl>>gnomad_constraint drugcentral: chembl_molecule, pubchem, uniprot, ensembl, hgnc, entrez # approved drugs -> targets/MOA + FDA/EMA/PMDA approval; reach via name/INN/InChIKey or compound (chembl_molecule/pubchem >> drugcentral) refseq: ensembl, entrez, taxonomy, ccds, uniprot, mirdb mirdb: refseq transcript: ensembl, exon, ufeature, alphamissense, civic_variant, gnomad_constraint, mavedb 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, alphamissense, cellosaurus, hpa, chembl_mechanism, ncrna_interaction, drugcentral, mavedb alphafold: uniprot interpro: uniprot, go, interproparent, interprochild chembl_molecule: mesh, chembl_activity, chembl_target, pubchem, chebi, clinical_trials, chembl_moleculeparent, chembl_moleculechild, chembl_mechanism, ncrna_drug, faers, drugcentral # parent=anhydrous/parent form, child=salt forms chembl_activity: chembl_molecule, chembl_assay, bao chembl_assay: chembl_activity, chembl_target, chembl_document, bao chembl_target: chembl_assay, uniprot, chembl_molecule, chembl_mechanism chembl_mechanism: chembl_molecule, chembl_target, uniprot, hgnc, ensembl # curated drug mechanism-of-action (incl. RNA therapeutics): drug >> chembl_mechanism, target/gene >> chembl_mechanism pubchem: chembl_molecule, chebi, hmdb, pubchem_activity, pubmed, patent_compound, bindingdb, ctd, pharmgkb, ncrna_drug, faers, drugcentral faers: chembl_molecule, pubchem, faers_reaction # openFDA FAERS drug->adverse-event; faers (per-drug master) -> faers_reaction children (PRR), reach via drug name or compound. NOTE co-occurrence not causation faers_reaction: faers # one per (drug,reaction): report_count, prr, serious_count, outcome; most-reported first pubchem_activity: pubchem, ensembl, uniprot chebi: pubchem, rhea, intact swisslipids: uniprot, go, chebi, uberon, cl lipidmaps: chebi, pubchem dbsnp: entrez, clinvar, pharmgkb_variant, alphamissense, spliceai, pharmgkb_var_annotation clinvar: hgnc, mondo, hpo, dbsnp, orphanet, civic_variant, cellosaurus, clingen_variant alphamissense: uniprot, transcript mavedb: uniprot, hgnc, ensembl, transcript # deep-mutational-scanning functional variant scores (ACMG PS3/BS3); reach via gene/protein >> mavedb; per-variant score + hgvs_pro + license # VARIANT-EFFECT SCORES — look up by the variant's OWN key with biobtree_entry(dataset=..), NOT via >>chains: # conservation key "chr:pos" (GRCh38) per-position phyloP / GERP / phastCons (also covers non-missense/splice positions) # gnomad_variant key "chr:pos:ref:alt" (GRCh38) gnomAD v4.1 genomes allele freq (af, grpmax, per-ancestry); also xrefs dbsnp # revel key "chr:pos:ref:alt" (GRCh38) REVEL ensemble missense pathogenicity (0-1, higher = pathogenic) # saprot key "uniprot:protein_variant" SaProt protein-LM variant effect (LLR <=0, lower = more damaging), e.g. P01116:G12D 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, civic, intogen, cellosaurus, doid, mim, ncit, umls, medgen, gard, sctid, icd9, icd10cm, icd10who, icd11, nando, meddra, nord, uberon, ncrna_disease, panelapp_gene # disease cross-refs + disease_has_location anatomy, from the Mondo OBO doid: mondo, alliance_disease, doidparent, doidchild # Disease Ontology (now a full ontology w/ hierarchy); reach MONDO + its disease graph via the mondo<->doid bridge alliance_disease: hgnc, mgi, rgd, zfin, sgd, wormbase, flybase, xenbase, doid, pubmed # cross-species + human gene->disease (Alliance of Genome Resources); gene >> alliance_disease >> doid, or doid >> alliance_disease >> mgi/rgd/... for model-organism genes alliance_phenotype: mgi, rgd, wormbase, xenbase, mp, wbphenotype, xpo, pubmed # model-organism gene -> OBSERVED knockout/mutant phenotypes (distinct from the upheno ontology-translation path). Reach from the model-organism gene directly: mgi/rgd/wormbase/xenbase >> alliance_phenotype >> mp gencc: mondo, hpo, hgnc, ensembl clingen_gene_validity: hgnc, entrez, ensembl, mondo # ClinGen gene-disease validity tier (Definitive..Refuted) + MOI clingen_dosage: entrez, hgnc, ensembl, mondo, mim, pubmed # ClinGen haploinsufficiency/triplosensitivity per gene clingen_variant: clinvar, hgnc, entrez, ensembl, mondo, pubmed # ClinGen VCEP ACMG variant pathogenicity (clinvar bridges to dbsnp) panelapp: panelapp_gene # Genomics England clinical gene panels (per-panel master); panel >> panelapp_gene >> hgnc for the panel's genes panelapp_gene: panelapp, hgnc, ensembl, mim, mondo # one per (panel,gene), green/amber confidence + mode-of-inheritance; a gene's panels via >>hgnc (panelapp_gene) ; the panel's disease via mondo/mim 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 # pharmgkb = reverse drug→clinical edge (drug >> pharmgkb >> pharmgkb_clinical) pharmgkb_guideline: hgnc, pharmgkb pharmgkb_pathway: hgnc, pharmgkb pharmgkb_var_annotation: hgnc, entrez, ensembl, dbsnp, pubmed # per-publication variant-annotation evidence (finding sentence, PMID, significance, study stats) beneath pharmgkb_clinical; reach via gene or rsID 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 hpa: ensembl, uniprot, hgnc, entrez, go, uberon, hpa_expression, hpa_pathology, hpa_antibody # Human Protein Atlas gene card: subcellular location (→go), specificity calls, top tissues hpa_expression: hpa, uberon, cellosaurus # per (gene,tissue/cell-line) RNA nTPM + IHC staining; reach genes-in-a-tissue via uberon >> hpa_expression hpa_pathology: hpa # per (gene,cancer) prognostic survival association hpa_antibody: hpa, ensembl # HPA validation antibody (reliability, antigen) rnacentral: uniprot, ensembl, intact, hgnc, refseq, ena, go # go = Rfam-projected GO annotations; rfam_id/rfam_description are attrs on the entry ncrna_disease: hgnc, ensembl, mondo, efo, pubmed # curated ncRNA->disease (LncRNADisease + HMDD); reach from the ncRNA gene ncrna_interaction: hgnc, ensembl, uniprot, pubmed # experimentally-supported ncRNA->protein interactions (NPInter) ncrna_drug: hgnc, ensembl, chembl_molecule, pubchem, pubmed # ncRNA drug-resistance / drug-target (ncRNADrug) reactome: ensembl, uniprot, chebi, go, reactomeparent, reactomechild rhea: chebi, uniprot, go go: ensembl, uniprot, reactome, msigdb, swisslipids, bgee, interpro, goparent, gochild, hpa, rnacentral hpo: clinvar, gencc, mondo, msigdb, orphanet, mim, hmdb, hgnc, hpoparent, hpochild, upheno efo: gwas, mondo, cellxgene, efoparent, efochild, ncrna_disease upheno: hpo, mp, zp, xpo, wbphenotype, fypo, uphenoparent, uphenochild # cross-species phenotype hub. A GENE's model-organism phenotypes are reached THROUGH hpo (genes are NOT linked directly to mp/upheno): >>hgnc>>hpo>>upheno>>mp (mouse), >>hgnc>>hpo>>upheno>>zp (zebrafish), ...>>xpo/wbphenotype/fypo. So gene->human HP phenotypes -> their cross-species equivalents. mp: upheno, mpparent, mpchild, alliance_phenotype # Mammalian Phenotype Ontology (mouse/rat). Reach from a gene via >>hgnc>>hpo>>upheno>>mp (NOT >>hgnc>>mp); observed model phenotypes via alliance_phenotype. zp: upheno, zpparent, zpchild # Zebrafish Phenotype Ontology. Reach from a gene via >>hgnc>>hpo>>upheno>>zp. xpo: upheno, xpoparent, xpochild, alliance_phenotype # Xenopus Phenotype Ontology wbphenotype: upheno, wbphenotypeparent, wbphenotypechild, alliance_phenotype # C. elegans Phenotype Ontology fypo: upheno, fypoparent, fypochild # Fission Yeast Phenotype Ontology uberon: bgee, cellxgene, cellxgene_celltype, swisslipids, uberonparent, uberonchild, hpa, hpa_expression 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, panelapp_gene 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 civic: entrez, ensembl, civic_variant, civic_evidence, civic_assertion # clinical interpretation of cancer variants civic_variant: civic, clinvar, civic_evidence, civic_assertion, transcript civic_evidence: civic_variant, civic, mondo, chembl_molecule, pubmed, clinical_trials civic_assertion: civic_variant, civic, mondo, chembl_molecule intogen: hgnc, entrez, ensembl, mondo, pubmed # cancer driver genes cellosaurus: taxonomy, uniprot, hgnc, mondo, orphanet, clinvar, dbsnp, uberon, cl, chebi, doi, patent, pubmed, depmap_dependency, hpa_expression # cell lines (CVCL) generif: entrez, pubmed # NCBI cited per-gene functional claims (RAG grounding) depmap: entrez, hgnc, ensembl # CRISPR gene essentiality aggregate (cancer dependency / target tractability) depmap_dependency: entrez, cellosaurus # per cell-line gene dependency (effect < -0.5) 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 interactions

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• search_finnish_statutesA

  Velvoite — EU Financial Regulatory ComplianceA

  Return Finlex search URL for Finnish statute keyword search. Finlex has no public JSON search API — returns the search URL for Claude to fetch. Args: query: Search terms in Finnish or English (e.g. 'kilpailukielto', 'non-compete').

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• get_summaryA

  PubmedA

  Resolve PubMed IDs (from search_pubmed) to citation metadata: title, authors (plain name strings), journal, publication date, DOI, and author_details[] with per-author detail (name, affiliations[] verbatim from the MEDLINE record, and any emails[] found inside those affiliation strings — empty arrays when the record has none), index-aligned with authors[]. Batch up to ~200 IDs per call — pass the array search_pubmed returned, or a comma-separated string — much cheaper than calling per-ID. Use when you have PMIDs and need the citation or a corresponding author's institution/contact; for the abstract text use get_abstract instead.

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• wikidata_resolve_external_idA

  wikidata-mcp-serverA

  Look up a Wikidata entity by an external identifier such as a DOI, PubMed ID, ORCID iD, or OpenAlex ID. Returns match=<entity> on success, match=null when not found, and match=null with multipleMatches populated when a Wikidata data integrity issue causes more than one entity to claim the same external ID. Common cross-server join use cases: CrossRef DOI → Wikidata paper QID (P356), PubMed PMID → Wikidata paper QID (P698), ORCID → author QID (P496), OpenAlex ID → entity QID (P10283). The property must be one whose Wikidata data type is external-id — item-valued or media properties (e.g. P31 instance-of, P18 image) are rejected rather than returning an empty match. Known value normalization is applied automatically: surrounding whitespace is trimmed, identifier-resolver URL prefixes are stripped (https://doi.org/, https://pubmed.ncbi.nlm.nih.gov/, https://orcid.org/), DOIs are uppercased, PMID prefixes stripped, ORCID hyphens normalized.

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• explore_topicA

  OpenArxA

  Map the conceptual landscape around a topic ACROSS THE PAPER CORPUS. Searches papers and their chunks, not the layer-2 claim graph — for published CLAIMS on a topic use methodist_explore_topic. Instead of returning a ranked list of papers, returns N distinct conceptual clusters with representative chunks. Built on keyConcept LLM-extracted markers diversification. Use for "what approaches exist to X" queries — answers with thematic map rather than ranked list. Better than search when you want breadth over depth. Temporal bias note: for topics with dense recent literature (e.g. current LLM research), the default ordering favors recent papers because vector similarity finds them first; specify dateTo for historical exploration of mature topics, or dateFrom+dateTo to slice a specific era. Diversification cap (maxClustersPerPaper) limits how many clusters can have the same source paper as representative chunk — protects against single-paper dominance.

  ConnectorAPI key

• openalex_resolve_nameA

  openalex-mcp-serverA

  Resolve a name or an identifier to an OpenAlex ID. ALWAYS use this before filtering by entity — names are ambiguous, IDs are not. A name returns up to 10 autocomplete matches with disambiguation hints. An identifier — OpenAlex ID, DOI, ORCID, ROR, PMID, or ISSN, bare or in URL form — resolves directly to the one record it addresses, and needs no entity_type. A PMCID is recognized as well, bare or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work's PMID or DOI instead.

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• orcid_get_worksA

  orcid-mcp-serverA

  Retrieve works associated with an ORCID iD — publications, datasets, software, preprints, and more. Returns work summaries with put-codes, titles, types, publication dates, journal names, and all external identifiers (DOIs, PMIDs, arXiv IDs, ISBNs). The first 50 works are returned by default; workCount reports the total available, and prolific records are paged with offset and the returned nextOffset (or raise limit). Set include_external_ids to false to omit identifier lists for a lighter payload. Pass the putCode from each work to orcid_get_work_detail to retrieve the full record including abstract and contributors. External IDs are ready for chaining to Crossref, PubMed, or arXiv servers. Works are self-reported; a researcher may not have linked all their publications.

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• check_citationsA

  pubscopeA

  Verify a pasted reference list (plain text, BibTeX or RIS) against Crossref, OpenAlex, DataCite, Semantic Scholar, arXiv, PubMed and DBLP, plus Retraction Watch. Flags references that cannot be found (possibly fabricated), retracted papers and DOI mismatches. One check per day without an account; sign in for more.

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• pubmed_publication_trendA

  PubmedA

  Count PubMed publications by year for a biomedical topic. Use for publication momentum, emerging-target activity, or whether a field is accelerating or cooling. Returns exact PubMed search counts for up to 10 calendar years; volume can reflect indexing and terminology changes and is not evidence quality or commercial validation.

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• search_cell_linesA

  can-immuneA

  Find cancer cell lines by name, ranked by mutation burden. Returns each matching cell line with its tissue of origin, cancer type, total mutations, unique mutant peptides, data sources (COSMIC / DepMap-CCLE / PubMed), and Cellosaurus ID. Covers only cell-line models (kept separate from primary tissue samples). Use before `get_cell_line` or `top_genes_in_cell_line`. Ordered by mutation count (most mutated first).

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• get_field_orientationA

  Scholar FeedA

  Returns CANDIDATE FOUNDATIONAL PAPERS for a research topic — cheap retrieval only, no synthesis. Ranks papers by a blend of citation count (0.6 weight, captures importance) and semantic similarity to your topic (0.4 weight). Use this to bootstrap a literature survey or get a fast sense of the landscape. For a synthesized orientation report (key concepts, open problems, reading order), use the /field-guide skill which calls this tool internally. Does not require a Pro API key — no LLM calls are made.

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• pubmed_get_full_textA

  PubmedA

  Fetch the FULL TEXT of a biomedical paper from PubMed Central (the open-access subset) by PubMed ID. PREFER OVER get_abstract when you need methods/results/discussion, not just the abstract — "read the full paper", "what methods did <PMID> use", "extract details from the paper". Resolves the PMID to its PMC id and returns the article body text (capped ~40k chars). Only open-access articles are in PMC — returns has_full_text:false (use get_abstract) otherwise.

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• get_report_detailA

  CDC MMWR ReportsA

  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').

  ConnectorNo auth

• search_reviewsA

  Cochrane Medical ReviewsA

  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).

  ConnectorNo auth