| schema_overviewA | Explain the Reactome GKB schema so you can write correct SQL. Returns a primer on the class-table-inheritance model (the `DatabaseObject`
supertable, subclass tables sharing `DB_ID`, the `Class_2_attribute` link
tables, and the stable-id join), the most useful tables, key join recipes,
and the data release loaded. **Read this once before writing `query()` SQL.**
The same primer is also available as the `schema://reactome` MCP resource.
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| list_tablesA | List tables in the database with their (exact) row counts and engine. Args:
filter: If given, only tables whose name contains this substring
(case-insensitive). e.g. "_2_" for link tables, "Reference" for
reference-data tables.
limit: Max tables to return (default 500; the DB has 242).
Returns:
Dict `{count, tables: [{table, rows, engine}], truncated}`, ordered by
row count descending. Row counts are exact (all tables are MyISAM).
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| describe_tableA | Show the columns of a table: name, type, nullability, key, default, extra. Args:
table: Exact table name (see `list_tables`). e.g. "Pathway",
"Pathway_2_hasEvent", "DatabaseObject".
Returns:
Dict `{table, columns: [{name, type, nullable, key, default, extra}]}`.
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| queryA | Run a single READ-ONLY SQL statement against the Reactome DB. Accepts one `SELECT` / `WITH` / `SHOW` / `DESCRIBE` / `EXPLAIN` statement.
Writes are impossible (the connection is a SELECT-only user) and multiple
statements are rejected. If a `SELECT`/`WITH` has no `LIMIT`, one is injected
automatically. Call `schema_overview` first to learn the join patterns.
Args:
sql: The statement to run. Use parameter-free SQL; quote literals
normally. e.g. `SELECT d.DB_ID, d._displayName FROM DatabaseObject d
JOIN StableIdentifier si ON d.stableIdentifier = si.DB_ID
WHERE si.identifier = 'R-HSA-69278'`.
max_rows: Max rows to return (1-5000, default 200). Long text cells are
also truncated; `truncated` flags either kind.
Returns:
Dict `{columns, rows, row_count, truncated, sql}` where `rows` is a list
of lists aligned to `columns`, and `sql` is the statement actually run
(with any auto-injected LIMIT). On a bad statement or DB error, returns
`{"error": ...}`.
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| get_objectA | Fetch a full Reactome object, assembled across its inheritance chain. Resolves a stable id ('R-HSA-69278') or numeric `DB_ID`, then merges the
`DatabaseObject` core fields with the subclass-table attributes that share
the same `DB_ID` (e.g. a Pathway pulls in `Event` + `Pathway` columns).
Args:
id: An 'R-HSA-...' stable id or a numeric DB_ID.
Returns:
Dict `{DB_ID, _class, _displayName, stable_id, attributes: {...}}` where
`attributes` is the union of the subclass rows (leaf class wins on any
name clash). `{"error": ...}` if the id is unknown.
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| search_by_nameA | Search objects by _displayName. Args:
query: Text to look for in the display name.
classes: Optional `_class` filter, e.g. ["Pathway", "Reaction"].
limit: Max results (1-200, default 25).
anchored: If True, match `name LIKE 'query%'` (fast — uses the prefix
index). If False (default), match `'%query%'` — more thorough but a
full scan of the 1.86M-row supertable (~1-2s). There are no FULLTEXT
indexes, so prefer `anchored=True` and/or a `classes` filter for hot
paths.
Returns:
Dict `{count, anchored, results: [{DB_ID, _class, _displayName, stable_id}]}`.
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| get_pathway_eventsA | List the ordered child events (sub-pathways & reactions) of a pathway. Args:
id: A Pathway stable id ('R-HSA-69278') or numeric DB_ID.
Returns:
Dict `{pathway_DB_ID, count, events: [{rank, DB_ID, _class,
_displayName, stable_id}], truncated}`, ordered by `hasEvent_rank`.
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| get_participantsA | Get the inputs, outputs, and catalysts of a reaction-like event. Args:
id: A ReactionlikeEvent (Reaction/BlackBoxEvent/...) stable id or DB_ID.
Returns:
Dict `{reaction_DB_ID, inputs, outputs, catalysts}` where `inputs`/
`outputs` are physical-entity dicts and each `catalysts` entry also
carries `catalyst_activity_DB_ID` and the GO `activity` DB_ID. Empty
lists if the object isn't a reaction or has none.
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| get_referrersA | Reverse lookup: which objects point AT this one (the inverse navigation REST makes awkward). Scans a curated set of common containment relations — which pathways contain
this event, which complexes/sets contain this entity, which reactions consume
or produce it. **Best-effort, not exhaustive** (the schema has 132 link
tables; this checks the high-value ones).
Args:
id: A stable id or numeric DB_ID of the object being referred to.
attribute: Optionally restrict to one relationship label
(contained_in_pathway, component_of_complex, member_of_set,
input_to_reaction, output_of_reaction).
limit: Max referrers per relation (1-500, default 50).
Returns:
Dict `{object_DB_ID, referrers: [{relationship, via_table, DB_ID, _class,
_displayName, stable_id}], scanned, note}`.
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