search_reactome_entity
Search the Reactome knowledgebase by keyword to find pathways, reactions, proteins, and small molecules, returning ranked matches with stable IDs, entity types, and species filters.
Instructions
Search the Reactome pathway knowledgebase by keyword (name / fuzzy match).
Resolves a term (pathway / reaction / protein / complex / small-molecule name) to Reactome stable IDs. Matching is keyword/fuzzy — UNLIKE the exact-match ChEMBL search tools, so expect ranked, approximate hits.
RETURNS a dict {'total_count', 'has_more', 'results'} — NOT a bare list.
total_count is the number of records RETURNED (capped by limit);
has_more is true if more matched beyond the cap. Each result carries
'id' (stable Reactome stId, e.g. "R-HSA-109581"), 'name', 'type' (facet
type), 'exactType' (specific BioPAX-ish class), 'species' (list), and — only
when include_summation=True — 'summation' (≤240-char description). On
upstream failure returns {'error': ...} instead — CHECK FOR 'error' BEFORE
READING 'results'.
species and types are validated case-INSENSITIVELY against Reactome's
controlled vocabularies and normalized to canonical casing before dispatch:
the server-side filter is case-SENSITIVE and silently ignores a mis-cased
value (returning UNFILTERED results), so a mis-cased species used to lose
most hits. An unrecognized species/type now RAISES rather than silently
returning the wrong rows.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | ||
| rows | No | DEPRECATED alias for `limit` (the old name meant per-type rows). Passing both `limit` and `rows` with different values raises. | |
| term | No | ||
| limit | No | Maximum number of records returned overall (default 25). A true total cap, not per-type. | |
| query | No | Search string, e.g. "apoptosis", "TP53", "cell cycle". Accepts aliases: `search`, `term`, `keyword`, `keywords`, `search_term`, `name` (supplying two different values raises ValueError). | |
| types | No | Filter by entity type(s), case-insensitive; a string or list. Valid values: Cell, Chemical Compound, Complex, DNA Sequence, Drug, Genes and Transcripts, OtherEntity, Pathway, Polymer, Protein, RNA Sequence, Reaction, Set. Unknown values raise ValueError. | |
| search | No | ||
| keyword | No | ||
| species | No | Filter by species scientific name, case-insensitive (e.g. "Homo sapiens", "homo sapiens", "Mus musculus"). A single string or a list. Unrecognized names raise ValueError (96 species available; see reactome.org/ContentService/data/species/all). | |
| keywords | No | ||
| search_term | No | ||
| include_summation | No | When True, add a ≤240-char 'summation' description to each record. Default False keeps the payload small (a broad default search is ~hundreds of tokens instead of thousands). |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||