| searchA | Free-text search across the Reactome knowledgebase (Solr-backed). Matches pathways, reactions, physical entities, and reference molecules by
name, synonym, identifier, and cross-reference.
Args:
query: Search text (e.g. "TP53", "glycolysis", "apoptosis").
species: Optional species filter, e.g. "Homo sapiens".
types: Optional comma-separated type filter, e.g. "Pathway,Reaction"
or "Protein".
rows: Max entries to return per type group (1-100).
start: Zero-based offset into the result set for pagination.
cluster: Group hits by type (recommended; keeps the response compact).
Returns:
Dict with `entries` (flattened `{stId, name, type, exactType, species,
referenceIdentifier, compartmentNames, databaseName, ...}` with HTML
highlight markup stripped), `entriesCount` (total matches), and
`resultTypes` (per-type match counts).
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| get_entryA | Fetch the full record for any Reactome object by identifier. Works for pathways, reactions, physical entities, complexes, regulators,
etc. Use `attribute` to retrieve a single field cheaply, or `enhanced` to
include indirect references.
Args:
stable_id: Reactome stable id (e.g. "R-HSA-69278") or numeric dbId.
enhanced: If True, query the `/data/query/enhanced/{id}` variant.
attribute: If set, fetch only this attribute (e.g. "displayName",
"speciesName", "stIdVersion").
max_chars: Size guard. If the JSON exceeds this, large nested fields
are replaced with a summary (default 50000).
Returns:
The object's JSON record (name, displayName, schemaClass, definition,
species, compartments, literatureReferences, etc.), size-guarded; or
`{stId, attribute, value}` when `attribute` is given.
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| get_entriesA | Batch-fetch records for several identifiers in one call (max 20). Args:
stable_ids: A list of identifiers, or a comma/whitespace-separated
string (e.g. "R-HSA-69278, R-HSA-69620").
Returns:
Dict `{count, entries}` where `entries` is the list of matched records.
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| list_top_level_pathwaysA | List the top-level pathways for a species (the browser's entry points). Args:
species: Species name ("Homo sapiens") or NCBI taxId ("9606").
Returns:
Dict `{count, pathways}` of top-level Pathway records.
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| list_pathway_eventsA | List every event (sub-pathway and reaction) contained in a pathway. Recurses the full sub-tree, so the result is the flattened set of events
beneath the given pathway.
Args:
stable_id: Pathway stable id, e.g. "R-HSA-69278".
Returns:
Dict `{count, events}` of Event records (Pathways + ReactionLikeEvents).
|
| get_event_ancestorsA | Retrieve all paths from an event up to its top-level pathway(s). Useful for building breadcrumbs / locating where a reaction sits.
Args:
stable_id: Event (pathway or reaction) stable id, e.g. "R-HSA-69620".
Returns:
Dict `{count, ancestors}` where each ancestor is an ordered path of
events from the queried event to a top-level pathway.
|
| get_event_participantsA | List the physical entities that participate in a reaction or pathway. Args:
stable_id: Event stable id, e.g. "R-HSA-69620".
Returns:
Dict `{count, participants}` grouping each participating PhysicalEntity
with its ReferenceEntities (UniProt/ChEBI/etc. cross-references).
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| find_pathways_for_entityA | Find the lower-level pathways that contain a given physical entity. The inverse of `list_pathway_events`: given a molecule/complex, which
pathways involve it?
Args:
stable_id: PhysicalEntity stable id, e.g. "R-HSA-199420".
species: Optional species name/taxId filter.
all_forms: If True, also match every other form of the entity (e.g.
phosphorylated/cleaved variants sharing a ReferenceEntity).
Returns:
Dict `{count, pathways}` of Pathway records that contain the entity.
|
| get_complex_subunitsA | List the subunits that constitute a complex (recursively). Args:
stable_id: Complex stable id, e.g. "R-HSA-83538".
exclude_structures: If True, omit structural sub-complexes.
Returns:
Dict `{count, subunits}` of the constituent PhysicalEntities.
|
| get_interactorsA | Fetch curated protein-protein interactors for an accession (IntAct). Args:
accession: A UniProt/ChEBI accession, e.g. "P04637".
page: 1-based page number; -1 (default) returns all.
page_size: Page size; -1 (default) returns all.
Returns:
The interactor summary object, including the list of interacting
accessions and their interaction scores.
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| list_speciesA | List the species annotated in Reactome. Args:
main_only: If True (default), return only the main curated species;
otherwise return every species including computational inferences.
Returns:
Dict `{count, species}` of Species records (name, taxId, abbreviation).
|
| list_diseasesA | List the diseases annotated in Reactome. Returns:
Dict `{count, diseases}` of Disease records (Disease Ontology terms).
|
| get_event_sbmlA | Export a pathway/reaction to SBML or SBGN, inline with size guarding. SBML connects Reactome straight into systems-biology tooling (and the
BioModels workflow). Large exports are head/tail truncated with a pointer
to `download_export` so multi-MB XML never floods the chat.
Args:
stable_id: Event stable id, e.g. "R-HSA-69620".
fmt: "sbml" (default) or "sbgn".
max_chars: Max characters to return inline (default 50000).
Returns:
Dict with `stId`, `format`, `mimeType`, `total_chars`, `truncated`, and
either `content` (full text) or `content_head` + `content_tail` +
`note` when truncated.
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| download_exportA | Stream a Reactome export to local disk and return the absolute path. Use this for any non-trivial payload (full SBML/SBGN, PDF documents, large
diagram images) instead of pulling it into the chat.
Args:
stable_id: Event/diagram/reaction stable id; for `kind="fireworks"` a
species name or taxId.
kind: One of "event" (sbml/sbgn), "diagram" (png/jpg/gif/svg),
"document" (pdf), "reaction" (png/jpg/gif/svg), or "fireworks"
(png/jpg/gif/svg, species-level overview).
ext: File extension valid for the chosen `kind`.
save_dir: Local directory to save into; created if absent.
Returns:
Absolute path to the saved file, or a string starting with "ERROR:".
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| analyze_identifiersA | Run pathway over-representation analysis on a gene/protein list. Submits identifiers (gene symbols, UniProt/ENSEMBL accessions, etc.) to the
Reactome AnalysisService and returns the most enriched pathways with their
statistics. Reuse the returned `token` with `get_analysis_results` to
page/sort/filter without re-submitting.
Args:
identifiers: A list, or whitespace/comma-separated string, of
identifiers (e.g. "TP53 EGFR BRCA1 MDM2 CDKN1A").
projection: If True (default), project non-human identifiers onto human
pathways (uses `/identifiers/projection`).
species: Optional species filter for the results.
sort_by: One of ENTITIES_PVALUE, ENTITIES_FDR, ENTITIES_RATIO, etc.
p_value: Keep pathways with entity p-value <= this (default 1.0 = all).
page_size: Pathways per page (default 20).
page: 1-based page number.
include_interactors: Expand the analysis with IntAct interactors.
Returns:
Dict with `token`, `pathwaysFound`, `identifiersNotFound`, and
`pathways` (each `{stId, name, species, entitiesFound, entitiesTotal,
pValue, fdr, reactionsFound, reactionsTotal}`), plus resource/species
summaries and any `warnings`.
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| get_analysis_resultsA | Retrieve (page/sort/filter) the results of a prior analysis by token. Args:
token: The `token` returned by `analyze_identifiers`.
species: Optional species filter.
sort_by: Sort key (e.g. ENTITIES_PVALUE, ENTITIES_FDR).
p_value: Keep pathways with entity p-value <= this.
page: 1-based page number.
page_size: Pathways per page.
resource: Identifier resource to score against (default "TOTAL").
Returns:
Same shape as `analyze_identifiers`.
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| get_analysis_not_foundA | List the submitted identifiers that did not map to any Reactome entity. Args:
token: The `token` returned by `analyze_identifiers`.
page: Zero-based page number.
page_size: Identifiers per page.
Returns:
Dict `{count, notFound}` of the unmapped identifiers.
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