$ doctrine orm:convert-mapping --filter="ms$ions" xml .

  [Doctrine\DBAL\DBALException]
  Unknown database type binary_float requested, Doctrine\DBAL\Platforms\OraclePlatform may not support it.

use Doctrine\Common\Annotations\AnnotationReader;
use Doctrine\Common\Annotations\AnnotationRegistry;

require_once 'Doctrine/Common/ClassLoader.php';

define('APPLICATION_ENV', "development");
error_reporting(E_ALL);

$classLoader = new \Doctrine\Common\ClassLoader('Doctrine');
$classLoader->register();

$config = new \Doctrine\ORM\Configuration();
$config->setProxyDir(__DIR__);
$config->setProxyNamespace('Proxies');

$config->setAutoGenerateProxyClasses((APPLICATION_ENV == "development"));

AnnotationRegistry::registerFile("Doctrine/ORM/Mapping/Driver/DoctrineAnnotations.php");
$reader = new AnnotationReader();
$driverImpl = new \Doctrine\ORM\Mapping\Driver\AnnotationDriver($reader, array(__DIR__ . "/../php/ru/niifhm/bioinformatics/biodb/model"));
$config->setMetadataDriverImpl($driverImpl);

if (APPLICATION_ENV == "development") {
    $cache = new \Doctrine\Common\Cache\ArrayCache();
} else {
    $cache = new \Doctrine\Common\Cache\ApcCache();
}

$config->setMetadataCacheImpl($cache);
$config->setQueryCacheImpl($cache);

$connectionOptions = array(
    'driver'   => 'oci8',
    'host'     => 'host.name',
    'dbname'   => 'db.name',
    'user'     => 'user.name',
    'password' => 'user.password'
);

$em = \Doctrine\ORM\EntityManager::create($connectionOptions, $config);
$platform = $em->getConnection()->getDatabasePlatform();
$platform->registerDoctrineTypeMapping('enum', 'string');

$em->getConfiguration()->setMetadataDriverImpl(
    new \Doctrine\ORM\Mapping\Driver\DatabaseDriver(
        $em->getConnection()->getSchemaManager()
    )
);

$helperSet = new \Symfony\Component\Console\Helper\HelperSet(array(
    'db' => new \Doctrine\DBAL\Tools\Console\Helper\ConnectionHelper($em->getConnection()),
    'em' => new \Doctrine\ORM\Tools\Console\Helper\EntityManagerHelper($em)
));