omnilab/reactome API reference

Omnilab\Reactome

ReactomeSource class

final class ReactomeSource extends HttpSource ReactomeSource.php:34

Reactome, the curated knowledgebase of biological pathways and reactions (EMBL-EBI, OICR, NYU, OHSU), through its Content Service: a pathway or a reaction by its stable identifier ("R-HSA-70171", glycolysis; "R-HSA-70420", a reaction of it) - its name and other names, species, summary, compartments, GO biological process, Rhea reaction, inputs and outputs, review status, release and update dates, DOI, its diagram; its participants as related things (the UniProt proteins and the ChEBI small molecules it involves), its organism, its sub-events and its inferred orthologous events; a search by text; the pathways or reactions of a protein or a molecule (pathways(), outside the contract: UniProt -> Reactome).

No key, no account, no published rate: no throttle by default. Two calls an entity (the event, its participants), one a search page.

const BASE_URI = 'https://reactome.org/ContentService/'

const MAX_LIMIT = 100

The most entries a search page holds.

ReactomeSource::__construct()

public function __construct(HttpClientInterface $http, readonly ?string $species = 'Homo sapiens', readonly bool $participants = true, string $baseUri = self::BASE_URI, array $headers = [], float $throttle = 0.0)

$species

the species a search and pathways() keep ("Homo sapiens", or a taxon id for pathways()); null: every species

$participants

whether entity() asks for the participants (a second call; thousands for a top-level pathway)

ReactomeSource::getName()

public function getName(): string

ReactomeSource::capabilities()

public function capabilities(): array

ReactomeSource::entity()

public function entity(Identifier|string $id): ?Entity

A pathway or a reaction by its stable identifier ("R-HSA-70171", versioned or not, "reactome:R-HSA-70171", its page); another base's identifier is refused before any call; null when Reactome has no such identifier, or when it names a physical entity (a protein, a complex, a molecule: not an event).

ReactomeSource::search()

public function search(Query $query): Page

The pathways and reactions whose text holds the words, Reactome's ranking, in the configured species; a domain other than biology answers nothing. An entity of a page holds what the search gives (its name, type, species, summary, compartments): entity() reads it whole.

ReactomeSource::pathways()

public function pathways(Identifier|string $participant, bool $reactions = false): array

The pathways (or the reactions) a protein or a small molecule takes part in, the lowest-level ones, in the configured species: a UniProt accession ("P68871", "uniprot:P68871") or a ChEBI id ("CHEBI:15422").

Outside the contract: the core asks one thing of a source, not the things another one is part of. Each entity holds its name, species and type: entity() reads it whole.

ReactomeSourceFactory class

final class ReactomeSourceFactory extends SourceFactory ReactomeSourceFactory.php:22

Reactome: pathways and reactions by stable identifier, their participants (UniProt proteins, ChEBI molecules), a search, and the pathways of a protein - no key needed.

options: mailto: 'support@glitchr.io' # in the User-Agent species: 'Homo sapiens' # what a search and pathways() keep; null: every species participants: true # entity() asks for the participants too (a second call) throttle: 0 # seconds between two calls: Reactome publishes no rate base_uri: 'https://reactome.org/ContentService/'

Options