README

One contract for the public science-data APIs, whatever the domain - chemistry, biology, species, astronomy, the Earth and its weather: what science knows of a thing, what it measures at a place, what it has catalogued over an area. Publications are not here: they are glitchr/omnischolar's.

$caffeine = $registry->get('pubchem')->entity('caffeine');
$caffeine->property('molecular_weight');             // 194.19 g/mol, from pubchem
$caffeine->identifier(Scheme::CHEBI);                // 27732: a cross-reference the Collector can follow

$caffeine = $collector->collect('pubchem', 'caffeine');   // then ChEBI and Wikidata, by its InChIKey and its CID
$caffeine->properties('molecular_weight');           // 194.19 g/mol from pubchem, 194.194 g/mol from chebi
$caffeine->property('melting_point');                // 234 °C, from wikidata

[$temperature] = $registry->get('open-meteo')->series(new SeriesQuery(['temperature_2m'], new Point(48.5734, 7.7521), $tomorrow, $tomorrow));
$temperature->max();                                 // 20.4, in $temperature->unit: °C

$scenes = $registry->get('copernicus')->products(new ProductQuery(['sentinel-2-l2a'], $strasbourg, new \DateTimeImmutable('-10 days'), maxCloudCover: 30));
$scenes->first()->preview;                           // the scene's thumbnail; its assets keep their hrefs

Every answer takes one of three shapes, not one per domain:

an entity (Model\Entity): a thing named and identified - a compound, a gene, a protein, a species, a star, an asteroid, an earthquake - its properties with their units (Property, Quantity), its synonyms, and its identifiers in other bases (Identifier, Scheme: PubChem CID, ChEBI, ChEMBL, InChIKey, CAS, UniProt, NCBI Gene and Taxonomy, Ensembl, PDB, GBIF, iNaturalist, SIMBAD, JPL SBDB, USGS events, Wikidata...); a time and a place for an event;
a series (Model\Series): one variable at a Point or over a BBox, its points in time, its unit, its step and aggregation;
a product (Model\Product, in the shape of a STAC item): a catalogued scene or file, its datetime, footprint, properties and assets.

This package holds the contract (Source\SourceInterface, Source\SourceFactory, Registry), the models, the Collector that follows an entity's cross-references into the other sources and the Merger that makes one entity of several, keeping the source of every property; and a bridge for Symfony. It needs no framework: it requires nothing but symfony/http-client-contracts, each source package symfony/http-client. Each source is a package of its own:

Package	Source	Shape	Key
`omnilab/pubchem`	PubChem (NCBI): compounds by CID, name, InChIKey, CAS, SMILES; computed properties, synonyms, 2D structure, cross-references	entity	none (5 calls a second at most)
`omnilab/open-meteo`	Open-Meteo: hourly, 15-minute and daily weather at a point, forecast and archive (from 1940)	series	none for non-commercial use
`omnilab/copernicus`	Copernicus Data Space: the STAC catalogue of Sentinel, Landsat, MODIS, the DEM and the Copernicus services	product	none to search (a CDSE token to download)
`omnilab/chebi`	ChEBI (EMBL-EBI): chemical entities by ChEBI id, InChIKey, CAS, KEGG or name; masses, structure, ontology (classes, roles), cross-references	entity	none
`omnilab/wikidata`	Wikidata: any item by Q-number, by a science base's identifier (PubChem, ChEBI, CAS, UniProt, NCBI...) or by label; labels in a language, cross-references, a few properties with units	entity	none (a User-Agent that names the caller; 200 calls a minute)
`omnilab/chembl`	ChEMBL (EMBL-EBI): bioactive molecules by ChEMBL id, InChIKey or name; development phase, computed properties, mechanisms of action and their targets, cross-references from UniChem	entity	none
`omnilab/uniprot`	UniProtKB: proteins by accession or entry name; function, gene, organism, sequence, mass, cofactors, ligands; their genes in NCBI and Ensembl	entity	none
`omnilab/gbif`	GBIF's taxonomy (the Catalogue of Life eXtended Release since 2026): taxa by key, legacy Backbone number, NCBI id or scientific name; status, IUCN category, lineage; NCBI cross-reference	entity	none
`omnilab/ncbi`	NCBI Gene and Taxonomy (Datasets v2, E-utilities): genes by GeneID, taxa by id or name; location, summary, lineage; UniProt, Ensembl and GBIF ids	entity	none (3 calls a second; 10 with an API key)

A source answers what it can - capabilities() says what - and throws NotSupportedException for the rest, before any call. Unknown is null, an empty page or a series without points; a service down or rate limited is an UnavailableException (RateLimitedException), which a caller never caches as "nothing".

Documentation

Plain PHP

composer require glitchr/omnilab omnilab/pubchem omnilab/open-meteo omnilab/copernicus omnilab/chebi omnilab/wikidata

use Omnilab\Chebi\ChebiSourceFactory;
use Omnilab\Copernicus\CopernicusSourceFactory;
use Omnilab\OpenMeteo\OpenMeteoSourceFactory;
use Omnilab\PubChem\PubChemSourceFactory;
use Omnilab\Registry;
use Omnilab\Wikidata\WikidataSourceFactory;
use Symfony\Component\HttpClient\HttpClient;

$http = HttpClient::create();   // or the application's client; a MockHttpClient in a test
$registry = new Registry([new PubChemSourceFactory($http), new ChebiSourceFactory($http), new WikidataSourceFactory($http), new OpenMeteoSourceFactory($http), new CopernicusSourceFactory($http)], [
    'pubchem' => ['factory' => 'pubchem', 'options' => ['mailto' => 'you@example.org']],
    'chebi' => ['factory' => 'chebi', 'options' => ['mailto' => 'you@example.org']],
    'wikidata' => ['factory' => 'wikidata', 'options' => ['mailto' => 'you@example.org', 'language' => 'fr']],
    'open-meteo' => ['factory' => 'open-meteo'],
    'copernicus' => ['factory' => 'copernicus'],
]);

No bundle, no container: a factory per source package, the registry built by hand. docs/installation.md opens on a whole script that runs as it is, against the real services.

Symfony

Omnilab\Bridge\Symfony\OmnilabBundle does that wiring in a Symfony application (docs/symfony.md); its components (symfony/config, symfony/dependency-injection, symfony/http-kernel) are not required by this package.

omnilab:
    sources:
        pubchem: { factory: pubchem, options: { mailto: '%env(OMNILAB_MAILTO)%' } }
        chebi: { factory: chebi, options: { mailto: '%env(OMNILAB_MAILTO)%' } }
        wikidata: { factory: wikidata, options: { mailto: '%env(OMNILAB_MAILTO)%', language: fr } }
        meteo: { factory: open-meteo }
        copernicus: { factory: copernicus }

public function __construct(SourceInterface $pubchem, SourceInterface $meteo, Collector $collector) {}

Docker: every source, for real

cd docker && cp .env.dist .env
docker compose run --rm omnilab sources
docker compose run --rm omnilab entity pubchem caffeine
docker compose run --rm omnilab collect pubchem caffeine   # then ChEBI and Wikidata, merged
docker compose run --rm omnilab series open-meteo 48.5734,7.7521 temperature_2m --from tomorrow --to tomorrow
docker compose run --rm omnilab products copernicus --point 48.5734,7.7521 --from=-10days --cloud 30
docker compose run --rm omnilab bare      # plain PHP: no bundle, no container, and what PHP loaded
docker compose run --rm omnilab test

License: MIT.

glitchr / omnilab

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README

Documentation

Plain PHP

Symfony

Docker: every source, for real