omnilab/opentargets API reference

Omnilab\OpenTargets

Association class

final readonly class Association Association.php:15

One association of Open Targets: a target (an Ensembl gene) and a disease or phenotype (EFO, Mondo, HPO, Orphanet), the overall score (0 to 1, the harmonic sum of the evidence) and the score of each data type that supports it (genetic_association, somatic_mutation, known_drug, affected_pathway, literature, rna_expression, animal_model, genetic_literature, clinical...).

public Identifier $target

public ?string $targetName

public ?Identifier $disease

null when the disease's id is in no scheme of the core (OTAR_...)

public string $diseaseId

public ?string $diseaseName

public float $score

public array $datatypes

the data types' scores, the strongest first

Association::__construct()

public function __construct(public Identifier $target, public ?string $targetName, public ?Identifier $disease, public string $diseaseId, public ?string $diseaseName, public float $score, public array $datatypes = [])

$disease

null when the disease's id is in no scheme of the core (OTAR_...)

$datatypes

the data types' scores, the strongest first

OpenTargetsSource class

final class OpenTargetsSource extends HttpSource OpenTargetsSource.php:36

The Open Targets Platform (EMBL-EBI, Wellcome Sanger, GSK and partners) through its GraphQL API: a target by its Ensembl gene ("ENSG00000244734", HBB) - its symbol, name, biotype, function, location, class, its UniProt and HGNC ids, its best associated diseases with their scores, its drugs and clinical candidates, its InterPro domains and Reactome pathways -; a disease or phenotype by its EFO, Mondo, HPO or Orphanet id ("MONDO_0011382", sickle cell disease) - its name, description, synonyms, therapeutic areas, parents, its ids in other ontologies, its best associated targets, its drugs -; a drug by its ChEMBL id - its type, stage, mechanisms of action and their targets, indications, trade names -; a search over the three; the associations themselves, paged (associations(), outside the contract).

No key, no account, no published rate: no throttle by default. One call an entity, one a search page.

const BASE_URI = 'https://api.platform.opentargets.org/api/v4/'

const MAX_LIMIT = 100

The most hits a search page holds.

OpenTargetsSource::__construct()

public function __construct(HttpClientInterface $http, readonly int $associations = 10, string $baseUri = self::BASE_URI, array $headers = [], float $throttle = 0.0)

$associations

how many associations (and drugs) an entity holds as properties, the best first

OpenTargetsSource::getName()

public function getName(): string

OpenTargetsSource::capabilities()

public function capabilities(): array

OpenTargetsSource::entity()

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

A target by its Ensembl gene ("ENSG00000244734"), a disease or a phenotype by its EFO, Mondo, HPO or Orphanet id ("MONDO_0011382", "MONDO:0011382", "EFO_0000305", "HP_0001878", "Orphanet_232"), a drug by its ChEMBL id ("CHEMBL4101807"); another base's identifier (an Ensembl transcript or protein among them) is refused before any call; null when Open Targets has no such thing.

OpenTargetsSource::search()

public function search(Query $query): Page

Targets, diseases and drugs matching a text, Open Targets' ranking; a domain other than biology answers nothing. An entity of a page holds its name and description: entity() reads it whole. A hit in no scheme of the core (a therapeutic area, OTAR_...) is left out.

OpenTargetsSource::associations()

public function associations(Identifier|string $id, int $limit = 25, ?string $cursor = null): Page

The associations of a target with diseases, or of a disease with targets, the best scored first, one page at a time (the cursor is the page's index). Outside the contract: an association is two things and a score.

OpenTargetsSourceFactory class

final class OpenTargetsSourceFactory extends SourceFactory OpenTargetsSourceFactory.php:20

Open Targets Platform: targets, diseases and drugs, their associations with scores, a search - no key needed.

options: mailto: 'support@glitchr.io' # in the User-Agent associations: 10 # associations (and drugs) an entity holds as properties, the best first throttle: 0 # seconds between two calls: Open Targets publishes no rate base_uri: 'https://api.platform.opentargets.org/api/v4/'

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