omnilab/rhea API reference

Omnilab\Rhea

RheaSource class

final class RheaSource extends HttpSource RheaSource.php:34

Rhea, the expert-curated knowledgebase of biochemical reactions (SIB, the reactions of UniProtKB's catalytic activities): a reaction by any of its four ids ("18157" the master, "18158" left to right, "18159" right to left, "18160" both ways), or by its KEGG reaction ("R00200") - its equation, status, balance, transport, its sides with their ChEBI participants and coefficients, its EC numbers, GO term, citations; its four ids and its KEGG reaction as identifiers; its ChEBI participants, EC numbers, GO term, Reactome events and the reviewed UniProt proteins that catalyse it as related things -; a search by text.

entity() asks Rhea's SPARQL endpoint once (the reaction, its quartet, its participants), then UniProt's REST API once for the reviewed proteins (unless enzymes is 0); search() asks Rhea's REST search. No key, no published rate; CC BY 4.0.

const BASE_URI = 'https://www.rhea-db.org/'

const SPARQL_URI = 'https://sparql.rhea-db.org/sparql'

const UNIPROT_URI = 'https://rest.uniprot.org/'

const MAX_LIMIT = 100

The most reactions a search page holds.

RheaSource::__construct()

public function __construct(HttpClientInterface $http, readonly int $enzymes = 25, string $baseUri = self::BASE_URI, readonly string $sparqlUri = self::SPARQL_URI, readonly string $uniprotUri = self::UNIPROT_URI, array $headers = [], float $throttle = 0.0)

$enzymes

how many reviewed UniProt proteins entity() asks for (a second call, to UniProt); 0: none

RheaSource::getName()

public function getName(): string

RheaSource::capabilities()

public function capabilities(): array

RheaSource::entity()

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

A reaction by a Rhea id ("18157", "RHEA:18160", its page) - a direction's id gives the master reaction, which carries all four - or by its KEGG reaction ("kegg.reaction:R00200", "rn:R00200"); another base's identifier is refused before any call; null when Rhea has none.

RheaSource::search()

public function search(Query $query): Page

The reactions Rhea's search finds for the text (a name, a ChEBI id, an EC number, "uniprot:P14618"...), in Rhea's order; a domain other than chemistry answers nothing. An entity of a page holds its equation, status, balance and participants: entity() reads it whole.

RheaSourceFactory class

final class RheaSourceFactory extends SourceFactory RheaSourceFactory.php:23

Rhea: biochemical reactions by Rhea or KEGG id, their ChEBI participants, EC numbers and the UniProt proteins that catalyse them; a search - no key needed.

options: mailto: 'support@glitchr.io' # in the User-Agent: Rhea asks callers for a contact address enzymes: 25 # reviewed UniProt proteins entity() asks for (a call to UniProt); 0: none throttle: 0 # seconds between two calls: Rhea publishes no rate base_uri: 'https://www.rhea-db.org/' sparql_uri: 'https://sparql.rhea-db.org/sparql' uniprot_uri: 'https://rest.uniprot.org/'

Options