tutor/bioontology

Bioontology Web Service Guzzle Client

Bioontology Web Service Guzzle Client

Provides an implementation of the Guzzle library to query NCBO Web Service., _(*1)

The goal of the National Center for Biomedical Ontology is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments., _(*2)

• https://www.bioontology.org/about-ncbo
• http://data.bioontology.org/documentation

API key

You must provide a valid API Key. Your API Key can be obtained by logging in at http://bioportal.bioontology.org/account, _(*3)

Usage

To use the Bioontology API Client simply instantiate the client., _(*4)

<?php

require dirname(__FILE__).'/../vendor/autoload.php';

use Tutor\Bioontology\BioontologyClient;
$client = BioontologyClient::factory(['apikey' => 'your_apikey']);

// if you want to see what is happening, add debug => true to the factory call
$client = BioontologyClient::factory(['apikey' => 'your_apikey', 'debug' => true]);

Invoke Commands using the __call method (auto-complete phpDocs are included), _(*5)

<?php

$client = BioontologyClient::factory(['apikey' => 'your_apikey']);
$response = $client->query([
  'q' => 'C0025202',
]);

Or Use the getCommand method (in this case you need to work with the $response['data'] array:, _(*6)

<?php

$client = BioontologyClient::factory();

// Retrieve the Command from Guzzle:
$command = $client->getCommand('Search', [
  'q' => 'C0025202',
]);
$command->prepare();

$response = $command->execute();

$data = $response['data'];

Examples

You can execute the examples in the examples directory., _(*7)

You can look at the services.json for details on what methods are available and what parameters are available to call them., _(*8)

http://data.bioontology.org/search?q=C0025202&ontologies=MESH, _(*9)

<?php

$client = BioontologyClient::factory(['apikey' => 'your_apikey']);
$response = $client->search([
  'q' => 'C0025202',
  'ontologies' => 'MESH',
]);

TODO

• [ ] Add some more examples
• [ ] Add tests
• [ ] Add other methods
• [ ] Add some Response models

Contributions welcome

Found a bug, open an issue, preferably with the debug output and what you did. Bugfix? Open a Pull Request and I'll look into it., _(*10)

License

The use Tutor\Bioontology\BioontologyClient API client is available under an MIT License., _(*11)