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PathwaysReactome ContentService

Reactome

Reactome is a curated database of biological pathways and reactions. Its pathways are linked to the proteins that take part in them by UniProt accession. Through ScholarMuse, an agent calls lookup_gene_protein with a gene symbol or UniProt accession and gets the Reactome pathways that protein is mapped to, with stable ids, names and a flag for disease pathways.

ScholarMuse tools: lookup_gene_protein. Each successful call uses credits.

Use in my agent

Ask your agent

Which Reactome pathways is human MTOR part of?
Is KRAS in any Reactome disease pathways? Give me the pathway ids.
How many Reactome pathways is UniProt P38398 (BRCA1) mapped to?

What your agent gets back

Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from Reactome.

lookup_gene_protein

Reactome fills the `pathways` list of the merged record. It is fetched only when a UniProt accession was resolved and `include` contains pathways (the default).

pathways[].id
Reactome stable id, for example R-HSA-165159
pathways[].name
Pathway name
pathways[].disease
True when Reactome marks it as a disease pathway
pathways[].url
URL of the pathway page at Reactome
pathwaysTotal
Number of pathways found before the cut to 15

What it covers

  • Pathways that a UniProt protein is mapped to in Reactome, for the organism of the lookup (human by default).
  • Each pathway comes with its stable id, name, disease flag and a link to the Reactome page.

Limits

  • At most 15 pathways are returned per call. pathwaysTotal gives the full count.
  • Lookup is by protein only. You cannot search Reactome by pathway name or keyword through this tool.
  • No reactions, participants, pathway hierarchy, diagrams or enrichment analysis are returned.
  • A protein that Reactome has not annotated, or a query with no UniProt accession, gives an empty pathways list.

How ScholarMuse reaches Reactome

The connector calls the Reactome ContentService directly, using the mapping endpoint that lists pathways for a UniProt accession in one species. No API key is sent.

Responses are cached for up to 7 days, so a new Reactome release can take that long to appear.

API key: the upstream API can be called without one, so you do not add one.

Licence and attribution

Licence: CC0-1.0 (data); pathway illustrations CC BY 4.0

Pathway data from Reactome (reactome.org).

Records that come from Reactome carry this licence and attribution. When you cite the data in a paper, follow Reactome's own citation guidance.

Capabilities that use Reactome

Gene & protein lookupNew

Gene & protein lookup

Life sciences & medicine · NCBI Gene, Ensembl, UniProt +5

Related sources

NCBI GeneEnsemblUniProtInterProGTExNCBI GEOSTRING

FAQ

ScholarMuse is not an official Reactome product. It is one MCP server for academic data, and its lookup_gene_protein tool queries Reactome. An agent connected to ScholarMuse can use Reactome without a separate server.

No. The Reactome API can be called without a key, and ScholarMuse does not ask you for one. You sign in to ScholarMuse once and your agent calls the tool.

The connector calls the Reactome ContentService directly, using the mapping endpoint that lists pathways for a UniProt accession in one species. No API key is sent. Responses are cached for up to 7 days, so a new Reactome release can take that long to appear.

CC0-1.0 (data); pathway illustrations CC BY 4.0. Attribution: Pathway data from Reactome (reactome.org). Records that come from Reactome carry this licence and attribution.

Yes. Each successful call to lookup_gene_protein uses credits, and a call that fails is not charged. Current price: Gene & protein lookup, 1 credit / call.