omnilab/chembl API reference

Omnilab\Chembl

ChemblSource class

final class ChemblSource extends HttpSource ChemblSource.php:38

ChEMBL, the EMBL-EBI's database of bioactive molecules with drug-like properties, through its data web services (www.ebi.ac.uk/chembl/api/data): a molecule by its ChEMBL id, its InChIKey or its name; its type, its maximum development phase, its computed properties (weight, ALogP, polar surface, hydrogen bond donors and acceptors, Lipinski's rule of five), its structure, its mechanisms of action and their targets, and its identifiers in ChEBI, PubChem and the other bases, which ChEMBL keeps in UniChem; a search by text or InChIKey.

No key, no account. A molecule costs one call, then one to UniChem for its cross-references and one or two for its mechanisms and their targets (each can be turned off).

const BASE_URI = 'https://www.ebi.ac.uk/chembl/api/data/'

const UNICHEM_URI = 'https://www.ebi.ac.uk/unichem/api/v1/compounds'

const MAX_PER_PAGE = 100

The most molecules one search page is asked for (ChEMBL's own cap is 1000).

ChemblSource::__construct()

public function __construct(HttpClientInterface $http, readonly int $synonyms = 20, readonly bool $unichem = true, readonly bool $mechanisms = true, string $baseUri = self::BASE_URI, readonly string $unichemUri = self::UNICHEM_URI, array $headers = [], float $throttle = 0.0)

$synonyms

how many synonyms to keep (0: none)

$unichem

ask UniChem for the identifiers of other bases (one call)

$mechanisms

ask the mechanisms of action and their targets (one or two calls)

ChemblSource::getName()

public function getName(): string

ChemblSource::capabilities()

public function capabilities(): array

ChemblSource::entity()

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

ChemblSource::search()

public function search(Query $query): Page

ChEMBL's search: an InChIKey (or its first block, the skeleton) is matched on the standard InChIKeys, any other text by the full-text search over names, synonyms and ids, the best first. Each molecule is read from the search's records: entity() adds the cross-references and the mechanisms.

ChemblSourceFactory class

final class ChemblSourceFactory extends SourceFactory ChemblSourceFactory.php:24

ChEMBL: bioactive molecules, their development phase, computed properties, mechanisms and targets, and their identifiers in other bases (through UniChem) - no key needed.

options: mailto: 'support@glitchr.io' # in the User-Agent: whom the EBI writes to before it blocks a caller synonyms: 20 # how many synonyms to keep (0: none) unichem: true # the identifiers of ChEBI, PubChem, UNII, DSSTox from UniChem (one call) mechanisms: true # the mechanisms of action and their targets (one or two calls) throttle: 0 # seconds between two calls: the EBI publishes no figure for ChEMBL base_uri: 'https://www.ebi.ac.uk/chembl/api/data/' unichem_uri: 'https://www.ebi.ac.uk/unichem/api/v1/compounds'

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