public function __construct( $collectionId, $collectionName, $languageId, $collectionType = "" ) {
$this->collectionId = $collectionId;
$this->languageId = $languageId;
if ( $this->collectionId == 0 )
$this->collectionId = bootstrapCollection( $collectionName, $languageId, $collectionType );
$this->contents = getCollectionContents( $this->collectionId );
}
function importUMLSFromDatabase( $server, $databaseName, $userName, $password, $sources = null ) {
$result = new UMLSImportResult;
openDatabase( $server, $databaseName, $userName, $password );
$languageId = 85;
echo "Creating UMLS collections\n";
$umlsCollectionId = bootstrapCollection( "UMLS", $languageId, "" );
$result->umlsCollectionId = $umlsCollectionId;
$relationCollectionId = bootstrapCollection( "UMLS Relation Types 2005", $languageId, "RELT" );
addDefinedMeaningToCollection( getCollectionMeaningId( $relationCollectionId ), $umlsCollectionId, "rel" );
$relationAttributesCollectionId = bootstrapCollection( "UMLS Relation Attributes 2005", $languageId, "RELT" );
addDefinedMeaningToCollection( $relationAttributesCollectionId, $umlsCollectionId, "rela" );
$semanticNetworkSemanticTypesCollectionId = bootstrapCollection( "Semantic Network 2005AC Semantic Types", $languageId, "CLAS" );
addDefinedMeaningToCollection( getCollectionMeaningId( $semanticNetworkSemanticTypesCollectionId ), $umlsCollectionId, "STY" );
$semanticNetworkRelationTypesCollectionId = bootstrapCollection( "Semantic Network 2005AC Relation Types", $languageId, "RELT" );
addDefinedMeaningToCollection( getCollectionMeaningId( $semanticNetworkRelationTypesCollectionId ), $umlsCollectionId, "RL" );
echo "Loading source abbreviations\n";
$sourceAbbreviations = loadSourceAbbreviations( $sources );
echo "Loading languages\n";
$isoLanguages = loadIsoLanguages();
echo "Importing UMLS terms per source\n";
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
$collectionId = bootstrapCollection( $source, $languageId, "" );
$result->sourceAbbreviations[$sab] = $collectionId;
echo " $i: $sab - $source\n";
importUMLSTerms( $sab, $umlsCollectionId, $collectionId, $languageId, $isoLanguages );
$i++;
}
echo "Importing UMLS definitions per source\n";
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " $i: $sab - $source\n";
importUMLSDefinitions( $sab, $umlsCollectionId, $result->sourceAbbreviations[$sab], $languageId );
$i++;
}
echo "Importing UMLS relation types\n";
importUMLSRelationTypes( $relationCollectionId, $languageId );
echo "Importing UMLS attribute types\n";
importUMLSRelationAttributes( $relationAttributesCollectionId, $languageId );
echo "Importing UMLS relations per source\n";
$relationCollection = getCollectionContents( $relationCollectionId );
$relationAttributesCollection = getCollectionContents( $relationAttributesCollectionId );
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " $i: $sab - $source\n";
$query = "select cui1, cui2, rel from MRREL where sab like '$sab'";
importUMLSRelations( $umlsCollectionId , $relationCollection, $query );
$query = "select cui1, cui2, rela from MRREL where sab like '$sab' and rela!=''";
importUMLSRelations( $umlsCollectionId , $relationAttributesCollection, $query );
$i++;
}
echo "Importing semantic network types\n";
importSNTypes( $semanticNetworkSemanticTypesCollectionId, "SELECT semtypeab,type,definition FROM srdef WHERE type='STY'", $languageId );
importSNTypes( $semanticNetworkRelationTypesCollectionId, "SELECT semtypeab,type,definition FROM srdef WHERE type='RL'", $languageId );
echo "Importing semantic network relations\n";
importSemanticTypeRelations( $semanticNetworkSemanticTypesCollectionId, $relationCollection, "SELECT SEMTYPE1, RELATION, SEMTYPE2 from semtypehier" );
importSemanticTypeRelations( $semanticNetworkRelationTypesCollectionId, $relationCollection, "SELECT RELTYPE1, RELATION, RELTYPE2 from semrelhier" );
echo "Importing UMLS semantic type relations per source\n";
$attributeTypes = getCollectionContents( $semanticNetworkSemanticTypesCollectionId );
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " " . $i++ . ": $sab - $source\n";
importUMLSSemanticTypes( $sab, $umlsCollectionId, $attributeTypes );
}
return $result;
}
