search_reactome_entity
Search Reactome biological pathways, reactions, and entities by keyword. Filter results by species and entity type to find relevant pathway components.
Instructions
Search the Reactome knowledgebase using keyword search.
Args:
query: The search query string (e.g., "apoptosis", "TP53", "cell cycle").
Accepts aliases: search, term, keyword, keywords,
search_term, name. If both query and an alias are given with
different values, this raises ValueError (pass only one).
species: Filter by species. Must be the scientific name
(e.g., "Homo sapiens", "Mus musculus"). Numeric NCBI taxon
IDs like "9606" are rejected here (this tool raises ValueError)
because the Reactome API silently ignores them AND can
degrade co-occurring filters (e.g. types). Accepts a
single string or a list of strings.
types: Filter by entity type(s). Accepts a single string (e.g.,
"Pathway") or a list (e.g., ["Pathway", "Reaction", "Complex"]).
Validated case-insensitively against the Reactome type enum;
unknown values raise ValueError (the API would otherwise silently
ignore them and return unfiltered results). Valid values:
Complex, Protein, Reaction, Set, Pathway, Genes and Transcripts,
Chemical Compound, DNA Sequence, Polymer, Drug, RNA Sequence,
OtherEntity, Cell.
rows: Per-category result cap. Reactome clusters results by
entity type (cluster=true), so rows=30 returns up to 30
hits per type, not 30 hits total. To bound the total,
constrain types to a single value.
Returns: JSON string: a bare array of results, each with 'id', 'name', and 'type' fields. Empty and non-empty results share the same shape. Example: '[{"id": "R-HSA-109581", "name": "Apoptosis", "type": "Pathway"}]'
Raises:
ValueError: If query is blank or types/species are invalid.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | ||
| rows | No | ||
| term | No | ||
| query | No | ||
| types | No | ||
| search | No | ||
| keyword | No | ||
| species | No | ||
| keywords | No | ||
| search_term | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |