About TogoMCP (UniProt, ChEMBL, PubChem, PDB, Reactome, NCBI)
Run by DBCLS, the Japanese Database Center for Life Science. Keyword search into UniProt, ChEMBL (targets and molecules), PubChem, PDBj, Reactome, Rhea and MeSH; NCBI E-utilities for Gene, ClinVar, Nucleotide and more; TogoID conversion between database identifiers; TogoVar human variant frequencies; and read-only SPARQL over every database in the RDF Portal. Answers can take several seconds. Identifiers are returned with every hit so results can be verified at the source.
Questions you can ask TogoMCP
Type them into Kahubi’s chat once TogoMCP is connected.
“Give me the UniProt entry, known structures and Reactome pathways for human TP53.”
What comes back: The UniProt accession, PDB IDs and Reactome pathway IDs, each verifiable at the source.
“Convert these Ensembl gene IDs to UniProt accessions and NCBI Gene IDs.”
What comes back: An identifier mapping table produced with TogoID.
TogoMCP MCP tools
The 33 tools the TogoMCP server offers to Kahubi. The assistant picks the right one for each question.
TogoMCP_Usage_GuideReturns the TogoMCP Usage Guide (v7 core): the workflow the other TogoMCP tools are designed around, a catalog of every database with what it holds, and the query rules that kee...
get_sparql_endpointsGet the registered SPARQL endpoints: most on RDF Portal (https://rdfportal.org/), some run externally by the database's own provider (e.g.
run_sparqlRun a read-only SPARQL query on an RDF database.
get_graph_listGet a list of named graphs on a SPARQL endpoint.
get_MIE_file**At the start of any task, identify ALL databases needed and call this tool for EACH of them before writing any SPARQL queries.** Do not query a database until its MIE file has...
get_workflowRetrieve a TogoMCP workflow: a multi-step analysis protocol that drives the TogoMCP tools.
search_uniprot_entitySearch for a UniProt entity ID by query.
get_pubchem_compound_idGet the PubChem compound ID(s) (CID) for a compound name, via the PubChem PUG-REST name lookup (https://pubchem.ncbi.nlm.nih.gov/rest/pug/).
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get_compound_attributes_from_pubchemGet core attributes of one PubChem compound: IUPAC name, molecular formula, molecular weight, SMILES, InChI, its identifiers.org IRI and a structure-image URL.
search_pdb_entitySearch PDBj for structures, chemical components, or BIRD molecules.
search_mesh_descriptorFind MeSH descriptors whose label contains the query, via the NLM MeSH lookup API (https://id.nlm.nih.gov/mesh/lookup/descriptor).
search_reactome_entitySearch the Reactome pathway knowledgebase by keyword (name / fuzzy match).
search_rhea_entitySearch the Rhea reaction database by keyword and return matching reactions.
search_chembl_id_lookupResolve a name to ChEMBL IDs across several entity kinds in one call.
search_chembl_targetResolve a biological TARGET (protein/receptor/enzyme) to a ChEMBL ID.
search_chembl_moleculeResolve a DRUG / COMPOUND / MOLECULE (by name or structure) to a ChEMBL ID.
togoid_getAllRelationDiscover all available ID conversion routes between databases.
togoid_getRelationCheck if a specific ID conversion route exists and get its details.
togoid_getAllDatasetList all databases registered in TogoID with their ID formats.
togoid_getDatasetGet configuration for a specific database in TogoID.
togoid_identifyIdResolve a bare accession to the TogoID dataset key(s) it could belong to.
togoid_getDescriptionGet human-readable descriptions for all databases in TogoID (https://togoid.dbcls.jp/, DBCLS's ID-conversion service; API at https://api.togoid.dbcls.jp/config/descriptions).
togoid_convertIdConvert identifiers from one database to another.
togoid_countIdCheck how many of your IDs can be converted before doing bulk conversion.
ncbi_esearchSearch NCBI Entrez databases with E-utilities ESearch (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi) and return the matching record IDs, for use with ncbi_esummary...
ncbi_list_databasesList the NCBI Entrez databases these tools are tuned for (gene, taxonomy, clinvar, medgen, mesh, pubmed, PubChem compound/substance/assay, …), with a description, ID type, examp...
ncbi_esummaryFetch document summaries for known IDs from NCBI E-utilities ESummary (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi): title, names, organism, dates and similar pe...
ncbi_efetchFetch full records for known IDs from NCBI E-utilities EFetch (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi), e.g.
togovar_search_geneResolve a human gene symbol/alias to its HGNC ID for variant search.
togovar_search_diseaseResolve a disease term to MONDO / MedGen IDs for variant search.
togovar_search_variantSearch TogoVar for human genome variants with population frequencies.
pubcasefinder_rank_by_phenotypesRank rare diseases (or genes) by how well they match a set of HPO phenotypes.
pubcasefinder_get_case_reportsList published case reports for a rare disease, newest first.
Using TogoMCP in Kahubi
- Official server. Run by the organisation behind the database, so results come straight from the source.
- Cited, checkable answers. Results are treated as retrieved material and cited with the source’s own identifiers, so you can open every record the answer relied on.
- Your files stay private. Only the search the assistant writes for your question is sent to TogoMCP.
More life science sources
- Open Targets PlatformTarget–disease–drug associations with the evidence behind them, from EMBL-EBI.
- Protein structures (PDB, AlphaFold)Search experimental and predicted protein structures, find similar folds, track ligands and fetch annotations.
- NCBI E-utilitiesGene, ClinVar, dbSNP, Taxonomy, Nucleotide, Protein, PMC and other NCBI databases.
- GBIF (biodiversity occurrences)2.5 billion species occurrence records from museums, surveys and citizen science worldwide.
- iNaturalistCitizen-science observations with photos, research-grade identifications and places.
- UniProtThe universal protein knowledgebase: function, disease links, domains, locations and structures for every known protein.