public function initialize() {
$this->bootstrapConceptIds();
// Add concepts to classes
addDefinedMeaningToCollectionIfNotPresent( $this->proteinConceptId, $this->classCollectionId, "amino acid, peptide, or protein" );
addDefinedMeaningToCollectionIfNotPresent( $this->geneConceptId, $this->classCollectionId, "gene or genome" );
addDefinedMeaningToCollectionIfNotPresent( $this->organismConceptId, $this->classCollectionId, "organism" );
addDefinedMeaningToCollectionIfNotPresent( $this->functionalDomainConceptId, $this->classCollectionId, "functional domain" );
addDefinedMeaningToCollectionIfNotPresent( $this->organismSpecificProteinConceptId, $this->classCollectionId, "organism specific protein" );
addDefinedMeaningToCollectionIfNotPresent( $this->organismSpecificGeneConceptId, $this->classCollectionId, "organism specific gene" );
addDefinedMeaningToCollectionIfNotPresent( $this->enzymeCommissionNumberConceptId, $this->classCollectionId, "enzyme commission number" );
// Add concepts to relation types
addDefinedMeaningToCollectionIfNotPresent( $this->geneConceptId, $this->relationTypeCollectionId, "gene or genome" );
addDefinedMeaningToCollectionIfNotPresent( $this->isManifestationOfConceptId, $this->relationTypeCollectionId, "is manifestation of" );
addDefinedMeaningToCollectionIfNotPresent( $this->occursInConceptId, $this->relationTypeCollectionId, "occurs in" );
addDefinedMeaningToCollectionIfNotPresent( $this->activityConceptId, $this->relationTypeCollectionId, "performs" );
addDefinedMeaningToCollectionIfNotPresent( $this->biologicalProcessConceptId, $this->relationTypeCollectionId, "biological process" );
addDefinedMeaningToCollectionIfNotPresent( $this->molecularFunctionConceptId, $this->relationTypeCollectionId, "molecular function" );
addDefinedMeaningToCollectionIfNotPresent( $this->cellularComponentConceptId, $this->relationTypeCollectionId, "cellular component" );
// addDefinedMeaningToCollectionIfNotPresent($this->keywordConceptId, $this->relationTypeCollectionId, "keyword");
addDefinedMeaningToCollectionIfNotPresent( $this->consistsOfId, $this->relationTypeCollectionId, "consists of" );
addDefinedMeaningToCollectionIfNotPresent( $this->containsConceptId, $this->relationTypeCollectionId, "contains" );
addDefinedMeaningToCollectionIfNotPresent( $this->conceptualPartOfId, $this->relationTypeCollectionId, "conceptual part of" );
}
public function add( IdStack $idPath, $record ) {
$definedMeaningId = $idPath->getKeyStack()->peek( 0 )->definedMeaningId;
$collectionMeaningId = $record->collectionMeaning;
$internalId = $record->sourceIdentifier;
if ( $collectionMeaningId != 0 ) {
addDefinedMeaningToCollectionIfNotPresent( $definedMeaningId, $collectionMeaningId, $internalId );
}
}
function importUMLSTerms( $sab, $umlsCollectionId, $sourceCollectionId, $languageId, $isoLanguages ) {
global
$db;
$queryResult = mysql_query( "select str, cui, lat, code from MRCONSO where sab like '$sab'", $db );
$progressBar = new ProgressBar( mysql_num_rows( $queryResult ), 100 );
$collectionMeaningId = getCollectionMeaningId( $sourceCollectionId );
while ( $umlsTerm = mysql_fetch_object( $queryResult ) ) {
$definedMeaningId = getDefinedMeaningFromCollection( $umlsCollectionId, $umlsTerm->cui );
$string = str_replace( '_', ' ', substr( trim( $umlsTerm->str ), 0, 240 ) );
$expression = findOrCreateExpression( $string, $isoLanguages[strtolower( $umlsTerm->lat )] );
if ( !$definedMeaningId ) {
$definedMeaningId = addDefinedMeaning( $expression->id );
addDefinedMeaningToCollection( $definedMeaningId, $umlsCollectionId, $umlsTerm->cui );
}
$expression->assureIsBoundToDefinedMeaning( $definedMeaningId, true );
addDefinedMeaningToCollectionIfNotPresent( $definedMeaningId, $sourceCollectionId, $umlsTerm->code );
$progressBar->advance( 1 );
}
mysql_free_result( $queryResult );
$progressBar->clear();
}
