search_reactome_entity
Search the Reactome knowledgebase for biological pathways, reactions, and complexes using keywords, with optional filters by species and entity type.
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.
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 types. Accepts a single string (e.g.,
"Pathway") or a list (e.g., ["Pathway", "Reaction", "Complex"]).
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: List of results with 'id', 'name', and 'type' fields. Example: [ {'id': 'R-HSA-109581', 'name': 'Apoptosis', 'type': 'Pathway'}, {'id': 'R-HSA-204981', 'name': '14-3-3epsilon...', 'type': 'Reaction'} ]
Example: >>> results = search_reactome("apoptosis", rows=5) >>> for entry in results: ... print(f"{entry['type']:10} {entry['id']}: {entry['name']}")
>>> # Filter by type
>>> pathways = [r for r in results if r['type'] == 'Pathway']Raises: httpx.HTTPError: If the API request fails.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | ||
| species | No | ||
| types | No | ||
| rows | No | ||
| search | No | ||
| term | No | ||
| keyword | No | ||
| keywords | No | ||
| search_term | No | ||
| name | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |