KnowledgeBase – MCP tools

114,633 tools. Last updated 2026-04-21 19:05

artifact_fork
m2ml — AI-to-AI Knowledge Network
Fork an artifact into your own KnowledgeBase. Creates an independent copy under your authorship with a forkedFrom pointer preserved in metadata. Citations do not transfer — the fork starts at zero. Gives the original author +0.5 reputation. Cannot fork private artifacts or your own.
Connector
artifact_publish
m2ml — AI-to-AI Knowledge Network
Publish a new knowledge artifact to your KnowledgeBase. Artifacts are first-class — you do not need to belong to a Collection. BRONZE+ can publish. Every agent can contribute on day one. Rate-limited to 5/day (shared with artifact_update).
Connector
bc_get_available_ontologiesA
BioContextAI Knowledgebase MCP
Discover available biomedical ontologies with metadata to identify relevant terminology resources for research and data integration.
Apache 2.0
bc_search_drugs_by_therapeutic_classA
BioContextAI Knowledgebase MCP
Search FDA-approved drugs by therapeutic or pharmacologic class to identify medications for specific treatment approaches. Retrieve drug details including application information, products, and sponsor names.
Apache 2.0
bc_get_kegg_id_by_gene_symbolA
BioContextAI Knowledgebase MCP
Convert gene symbols to KEGG IDs for pathway analysis. Use this tool to map gene symbols from organisms like human, mouse, or yeast to their corresponding KEGG gene identifiers.
Apache 2.0
SearchGenAICDKConstructsA
AWS CDK MCP Server
Find AWS CDK constructs for generative AI by searching names, descriptions, or types. Dynamically fetches current documentation from GitHub repositories.
Apache 2.0

Matching MCP Servers

BioContextAI Knowledgebase MCPofficial
Bioinformatics Autonomous Agents Research & Data
biocontext-ai
A
security
A
license
B
quality
An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.
Last updated 2026-01-12
52
22
Apache 2.0
PDF Knowledgebase MCP Server
RAG Systems Vector Databases Knowledge & Memory
juanqui
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security
A
license
-
quality
A Model Context Protocol server that enables intelligent document search and retrieval from PDF collections, providing semantic search capabilities powered by OpenAI embeddings and ChromaDB vector storage.
Last updated 2025-09-15
11
MIT

bc_get_available_pharmacologic_classesA
BioContextAI Knowledgebase MCP
Retrieve available pharmacologic classes from FDA database to identify medication classification options for research or analysis purposes.
Apache 2.0
bc_get_uniprot_protein_infoA
BioContextAI Knowledgebase MCP
Retrieve protein details from UniProt database using protein ID, name, or gene symbol to access accession, sequence, functions, and organism information.
Apache 2.0
bc_get_drug_by_application_numberA
BioContextAI Knowledgebase MCP
Retrieve FDA-approved drug details using application numbers (NDA/ANDA/BLA format) to access verified information about products, sponsors, and application data.
Apache 2.0
bc_get_ensembl_id_from_gene_symbolA
BioContextAI Knowledgebase MCP
Convert gene symbols to Ensembl IDs for specified species to enable standardized gene identification in biomedical research.
Apache 2.0
bc_get_study_detailsA
BioContextAI Knowledgebase MCP
Retrieve comprehensive clinical trial details including study design, eligibility criteria, outcomes, locations, and contacts using an NCT ID.
Apache 2.0
bc_get_uniprot_id_by_protein_symbolA
BioContextAI Knowledgebase MCP
Find UniProt accession IDs using protein names and species taxonomy IDs to identify proteins in biological databases.
Apache 2.0
bc_query_open_targets_graphqlA
BioContextAI Knowledgebase MCP
Execute GraphQL queries to retrieve biomedical data on targets, diseases, drugs, and variants from the Open Targets API for research and analysis.
Apache 2.0
bc_get_human_protein_atlas_infoA
BioContextAI Knowledgebase MCP
Retrieve Human Protein Atlas data including tissue expression, subcellular localization, and pathology information using gene identifiers.
Apache 2.0
bc_get_string_idA
BioContextAI Knowledgebase MCP
Convert protein identifiers to STRING database IDs for reliable biomedical data integration. Maps gene names, synonyms, or UniProt IDs to standardized STRING identifiers.
Apache 2.0
bc_get_string_interactionsA
BioContextAI Knowledgebase MCP
Retrieve protein-protein interactions for a specified protein with customizable score thresholds to analyze molecular relationships in biological research.
Apache 2.0
bc_get_biorxiv_preprint_detailsA
BioContextAI Knowledgebase MCP
Retrieve detailed preprint metadata from bioRxiv or medRxiv using DOI to access title, authors, abstract, publication date, version, category, and license information.
Apache 2.0
bc_get_term_detailsA
BioContextAI Knowledgebase MCP
Retrieve detailed information about biomedical ontology terms including definitions, synonyms, and hierarchical relationships from verified knowledge bases.
Apache 2.0
bc_get_recent_biorxiv_preprintsA
BioContextAI Knowledgebase MCP
Retrieve recent bioRxiv/medRxiv preprints by date range, days, or count to access current biomedical research findings.
Apache 2.0
bc_get_interpro_entryA
BioContextAI Knowledgebase MCP
Retrieve detailed metadata for InterPro entries including family, domain, or functional site information from member databases like PFAM and PROSITE, with optional protein interactions, pathways, and cross-references.
Apache 2.0
bc_get_panglaodb_optionsA
BioContextAI Knowledgebase MCP
Retrieve available filter options for PanglaoDB marker genes, including unique organ and cell type values to refine biological data queries.
Apache 2.0
bc_get_open_targets_query_examplesA
BioContextAI Knowledgebase MCP
Retrieve example GraphQL queries for biomedical data exploration using the Open Targets API, demonstrating common use cases like target information, drug discovery, and disease associations.
Apache 2.0
bc_get_string_similarity_scoresA
BioContextAI Knowledgebase MCP
Calculate protein similarity scores using STRING database Smith-Waterman bit scores to assess homology between protein pairs for biomedical research.
Apache 2.0
bc_search_ontology_termsA
BioContextAI Knowledgebase MCP
Search biomedical ontologies to find standardized terms for genes, proteins, diseases, and chemicals. Use this tool to retrieve verified terminology from multiple biological databases.
Apache 2.0
bc_query_keggA
BioContextAI Knowledgebase MCP
Query the KEGG database to retrieve biological pathway, gene, compound, disease, and drug information for research analysis.
Apache 2.0
bc_get_studies_by_conditionA
BioContextAI Knowledgebase MCP
Search clinical trials by medical condition to find studies with breakdowns by status, study type, and phase for research planning.
Apache 2.0
bc_get_efo_id_by_disease_nameA
BioContextAI Knowledgebase MCP
Find EFO/Mondo/HP IDs for diseases to use in Open Targets queries by searching the OLS ontology with a disease name.
Apache 2.0
bc_search_studiesA
BioContextAI Knowledgebase MCP
Search clinical trials using filters for condition, intervention, sponsor, status, phase, study type, location, age, and sex to find relevant medical research studies.
Apache 2.0
bc_get_alphafold_info_by_protein_symbolA
BioContextAI Knowledgebase MCP
Retrieve AlphaFold protein structure predictions by converting protein symbols to UniProt IDs and fetching detailed structural data including PDB/CIF files and confidence scores.
Apache 2.0
bc_get_open_targets_graphql_schemaA
BioContextAI Knowledgebase MCP
Retrieve the GraphQL schema for Open Targets to construct precise queries for biomedical data exploration and analysis.
Apache 2.0
bc_get_europepmc_articlesA
BioContextAI Knowledgebase MCP
Search biomedical literature in Europe PMC by query, title, abstract, or author using logical operators to find relevant scientific articles with metadata.
Apache 2.0
bc_get_reactome_info_by_identifierB
BioContextAI Knowledgebase MCP
Retrieve biological pathways associated with a specific identifier from the Reactome database, with filtering options for species, significance, and pathway characteristics.
Apache 2.0
bc_get_europepmc_fulltextB
BioContextAI Knowledgebase MCP
Retrieve complete article XML from EuropePMC using PMC ID for biomedical text processing and analysis.
Apache 2.0
bc_search_pride_proteinsB
BioContextAI Knowledgebase MCP
Search for specific proteins within PRIDE mass spectrometry proteomics datasets using project accession numbers and optional keywords to identify proteins, genes, and modifications.
Apache 2.0
bc_get_antibody_informationB
BioContextAI Knowledgebase MCP
Retrieve detailed antibody specifications including catalog numbers, vendor, clonality, epitope, applications, and target species by providing an Antibody Registry ID.
Apache 2.0
bc_get_go_terms_by_geneB
BioContextAI Knowledgebase MCP
Retrieve Gene Ontology terms associated with specific genes to understand their biological functions, processes, and cellular components using structured vocabularies.
Apache 2.0
bc_search_interpro_entriesB
BioContextAI Knowledgebase MCP
Search InterPro protein family and domain entries by name, type, database, GO term, or species to retrieve matching entries with metadata from biomedical knowledge bases.
Apache 2.0
bc_search_google_scholar_publicationsB
BioContextAI Knowledgebase MCP
Search Google Scholar for academic publications using queries or author names to retrieve titles, authors, abstracts, and citation data for research purposes.
Apache 2.0
bc_get_pride_projectB
BioContextAI Knowledgebase MCP
Retrieve detailed metadata and experimental information for PRIDE mass spectrometry proteomics projects using project accession numbers.
Apache 2.0
bc_get_protein_domainsB
BioContextAI Knowledgebase MCP
Retrieve protein domain architecture and InterPro matches to analyze functional sites and structural organization from UniProt databases.
Apache 2.0
bc_get_recruiting_studies_by_locationB
BioContextAI Knowledgebase MCP
Find recruiting clinical trials by geographic location to identify research opportunities for patients or participants. Returns paginated results with study type, phase, and condition breakdowns.
Apache 2.0
bc_get_string_network_imageB
BioContextAI Knowledgebase MCP
Generate protein-protein interaction network visualizations from the STRING database for specific proteins and species, returning PNG images of biological networks.
Apache 2.0
bc_get_studies_by_interventionB
BioContextAI Knowledgebase MCP
Search clinical trials by drug or therapy name with filters for condition, phase, and status to find relevant studies with paginated results and breakdowns.
Apache 2.0
bc_count_drugs_by_fieldB
BioContextAI Knowledgebase MCP
Count unique values in FDA-approved drug fields for statistical analysis. Specify a field like 'sponsor_name' or 'dosage_form' to get term frequencies.
Apache 2.0
bc_get_term_hierarchical_childrenB
BioContextAI Knowledgebase MCP
Retrieve hierarchical child terms from biomedical ontologies to understand term relationships and structure in knowledge bases.
Apache 2.0
bc_get_drug_statisticsB
BioContextAI Knowledgebase MCP
Retrieve FDA drug database statistics including top sponsors, dosage forms, administration routes, and marketing statuses to analyze pharmaceutical data trends.
Apache 2.0
bc_get_cell_ontology_termsB
BioContextAI Knowledgebase MCP
Search for standardized cell ontology terms using controlled vocabulary to identify cell types like T cells or neurons in biomedical research.
Apache 2.0
bc_get_panglaodb_marker_genesC
BioContextAI Knowledgebase MCP
Retrieve marker genes from PanglaoDB dataset with filters for species, scores, organ, cell type, or gene symbol to identify cell-specific genetic markers.
Apache 2.0
bc_search_grants_govC
BioContextAI Knowledgebase MCP
Search for U.S. government grant opportunities using keywords, agencies, or eligibility criteria to find funding with deadlines and requirements.
Apache 2.0
bc_get_antibody_listC
BioContextAI Knowledgebase MCP
Search the Antibody Registry to find antibodies by gene symbol, protein name, or UniProt ID. Retrieve catalog numbers, vendors, clonality, applications, and metadata for research.
Apache 2.0
bc_get_generic_equivalentsC
BioContextAI Knowledgebase MCP
Find generic drug alternatives for brand-name medications by searching ANDA entries with matching active ingredients.
Apache 2.0

artifact_fork

artifact_publish

bc_get_available_ontologiesA

bc_search_drugs_by_therapeutic_classA

bc_get_kegg_id_by_gene_symbolA

SearchGenAICDKConstructsA

Matching MCP Servers

BioContextAI Knowledgebase MCPofficial

PDF Knowledgebase MCP Server

bc_get_available_pharmacologic_classesA

bc_get_uniprot_protein_infoA

bc_get_drug_by_application_numberA

bc_get_ensembl_id_from_gene_symbolA

bc_get_study_detailsA

bc_get_uniprot_id_by_protein_symbolA

bc_query_open_targets_graphqlA

bc_get_human_protein_atlas_infoA

bc_get_string_idA

bc_get_string_interactionsA

bc_get_biorxiv_preprint_detailsA

bc_get_term_detailsA

bc_get_recent_biorxiv_preprintsA

bc_get_interpro_entryA

bc_get_panglaodb_optionsA

bc_get_open_targets_query_examplesA

bc_get_string_similarity_scoresA

bc_search_ontology_termsA

bc_query_keggA

bc_get_studies_by_conditionA

bc_get_efo_id_by_disease_nameA

bc_search_studiesA

bc_get_alphafold_info_by_protein_symbolA

bc_get_open_targets_graphql_schemaA

bc_get_europepmc_articlesA

bc_get_reactome_info_by_identifierB

bc_get_europepmc_fulltextB

bc_search_pride_proteinsB

bc_get_antibody_informationB

bc_get_go_terms_by_geneB

bc_search_interpro_entriesB

bc_search_google_scholar_publicationsB

bc_get_pride_projectB

bc_get_protein_domainsB

bc_get_recruiting_studies_by_locationB

bc_get_string_network_imageB

bc_get_studies_by_interventionB

bc_count_drugs_by_fieldB

bc_get_term_hierarchical_childrenB

bc_get_drug_statisticsB

bc_get_cell_ontology_termsB

bc_get_panglaodb_marker_genesC

bc_search_grants_govC

bc_get_antibody_listC

bc_get_generic_equivalentsC