diff --git a/classes/ChecklistVoucherReport.php b/classes/ChecklistVoucherReport.php
index eac7448bfc..fb25ed3018 100644
--- a/classes/ChecklistVoucherReport.php
+++ b/classes/ChecklistVoucherReport.php
@@ -271,8 +271,6 @@ private function getMissingTaxaBaseSql($sqlFrag){
 	public function getMissingProblemTaxa(){
 		$retArr = Array();
 		if($sqlFrag = $this->getSqlFrag()){
-			//Make sure tidinterpreted are valid
-			//$this->conn->query('UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname SET o.tidinterpreted = t.tid WHERE o.tidinterpreted IS NULL');
 			//Grab records
 			$sql = 'SELECT DISTINCT o.occid, c.institutioncode, c.collectioncode, o.catalognumber, o.sciname, o.recordedby, o.recordnumber, o.eventdate, '.
 				'CONCAT_WS("; ",o.country, o.stateprovince, o.county, o.locality) as locality '.
diff --git a/classes/ImageLocalProcessor.php b/classes/ImageLocalProcessor.php
index 09f799fb8f..fb1708e450 100644
--- a/classes/ImageLocalProcessor.php
+++ b/classes/ImageLocalProcessor.php
@@ -1557,7 +1557,8 @@ private function updateCollectionStats(){
 
 			$this->logOrEcho('Cleaning house...');
 			$collString = implode(',',$this->collProcessedArr);
-			if(!$occurMain->generalOccurrenceCleaning($collString)){
+			$occurMain->setCollidStr($collString);
+			if(!$occurMain->generalOccurrenceCleaning()){
 				$errorArr = $occurMain->getErrorArr();
 				foreach($errorArr as $errorStr){
 					$this->logOrEcho($errorStr,1);
@@ -1570,7 +1571,8 @@ private function updateCollectionStats(){
 
 			$this->logOrEcho('Updating statistics...');
 			foreach($this->collProcessedArr as $collid){
-				if(!$occurMain->updateCollectionStats($collid)){
+				$occurMain->setCollidStr($collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);
diff --git a/classes/ImageProcessor.php b/classes/ImageProcessor.php
index 8ec52c8f55..0b13aaba43 100644
--- a/classes/ImageProcessor.php
+++ b/classes/ImageProcessor.php
@@ -347,7 +347,8 @@ public function loadFileData($postArr){
 				$occurMain = new OccurrenceMaintenance($this->conn);
 
 				$this->logOrEcho('Updating statistics...');
-				if(!$occurMain->updateCollectionStats($this->collid)){
+				$occurMain->setCollidStr($this->collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);
@@ -545,7 +546,8 @@ private function cleanHouse($collList){
 		/*
 		$this->logOrEcho('General cleaning...',2);
 		$collString = implode(',',$collList);
-		if(!$occurMain->generalOccurrenceCleaning($collString)){
+		$occurMain->setCollidStr($collString);
+		if(!$occurMain->generalOccurrenceCleaning()){
 			$errorArr = $occurMain->getErrorArr();
 			foreach($errorArr as $errorStr){
 				$this->logOrEcho($errorStr,1);
@@ -559,7 +561,8 @@ private function cleanHouse($collList){
 		if($collList){
 			$this->logOrEcho('Updating collection statistics...',2);
 			foreach($collList as $collid){
-				if(!$occurMain->updateCollectionStats($collid)){
+				$occurMain->setCollidStr($collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);
diff --git a/classes/OccurrenceCollectionProfile.php b/classes/OccurrenceCollectionProfile.php
index bdded68a8b..45965a91b8 100644
--- a/classes/OccurrenceCollectionProfile.php
+++ b/classes/OccurrenceCollectionProfile.php
@@ -507,6 +507,7 @@ public function getBasicStats(){
 
 	public function updateStatistics($verbose = false){
 		$occurMaintenance = new OccurrenceMaintenance();
+		$occurMaintenance->setCollidStr($this->collid);
 		if($verbose){
 			echo '<ul>';
 			$occurMaintenance->setVerbose(true);
@@ -514,13 +515,14 @@ public function updateStatistics($verbose = false){
 			flush();
 			ob_flush();
 		}
-		$occurMaintenance->generalOccurrenceCleaning($this->collid);
+		$occurMaintenance->generalOccurrenceCleaning();
+		$occurMaintenance->batchUpdateGeoreferenceIndex();
 		if($verbose){
 			echo '<li>Updating statistics...</li>';
 			flush();
 			ob_flush();
 		}
-		$occurMaintenance->updateCollectionStats($this->collid, true);
+		$occurMaintenance->updateCollectionStatsFull();
 		if($verbose){
 			echo '<li>Finished updating collection statistics</li>';
 			flush();
@@ -602,7 +604,8 @@ public function batchUpdateStatistics($collId){
 				echo '<li style="margin-left:15px;">Cleaning statistics for: '.$r->collectionname.'</li>';
 				flush();
 				ob_flush();
-				$occurMaintenance->updateCollectionStats($r->collid, true);
+				$occurMaintenance->setCollidStr($r->collid);
+				$occurMaintenance->updateCollectionStatsFull();
 			}
 			$rs->free();
 			echo '<li>Statistics update complete!</li>';
diff --git a/classes/OccurrenceMaintenance.php b/classes/OccurrenceMaintenance.php
index 6b495dd3b3..a45de65fca 100644
--- a/classes/OccurrenceMaintenance.php
+++ b/classes/OccurrenceMaintenance.php
@@ -5,6 +5,7 @@ class OccurrenceMaintenance {
 
 	protected $conn;
 	private $destructConn = true;
+	private $collidStr = null;
 	private $verbose = false;	// 0 = silent, 1 = echo as list item
 	private $errorArr = array();
 
@@ -27,71 +28,35 @@ public function __destruct(){
  	}
 
 	//General cleaning functions
-	public function generalOccurrenceCleaning($collId){
+	public function generalOccurrenceCleaning(){
 		set_time_limit(600);
 		$status = true;
 
-		/*
-		$this->outputMsg('Updating null families of family rank identifications... ',1);
-		$occidArr = array();
-		$sql = 'SELECT occid FROM omoccurrences WHERE (family IS NULL) AND collid IN('.$collId.') AND (sciname LIKE "%aceae" OR sciname LIKE "%idae")';
-		$rs = $this->conn->query($sql);
-		while($r = $rs->fetch_object()){
-			$occidArr[] = $r->occid;
-		}
-		$rs->free();
-		if($occidArr){
-			$sql = 'UPDATE omoccurrences SET family = sciname WHERE occid IN('.implode(',',$occidArr).')';
-			if(!$this->conn->query($sql)){
-				$this->errorArr[] = 'WARNING: unable to update family; '.$this->conn->error;
-				if($this->verbose) $this->outputMsg($this->errorArr,2);
-				$status = false;
-			}
-		}
-		unset($occidArr);
-		*/
+		$this->indexOccurrencesToTaxa();
 
 		//Update NULL sciname with family designations when family field is not null
 		$occidArr = array();
 		$this->outputMsg('Updating null scientific names of family rank identifications... ',1);
-		$sql = 'SELECT occid FROM omoccurrences WHERE family IS NOT NULL AND sciname IS NULL AND collid IN('.$collId.')';
-		$rs = $this->conn->query($sql);
-		while($r = $rs->fetch_object()){
-			$occidArr[] = $r->occid;
-		}
-		$rs->free();
-		if($occidArr){
-			$sql = 'UPDATE omoccurrences SET sciname = family WHERE occid IN('.implode(',',$occidArr).') ';
-			if(!$this->conn->query($sql)){
-				$errStr = 'WARNING: unable to update sciname using family; '.$this->conn->error;
-				$this->errorArr[] = $errStr;
-				if($this->verbose) $this->outputMsg($errStr,2);
-				$status = false;
-			}
-		}
-		unset($occidArr);
-
-		//Update tidInterpreted values by matching on sciname
-		$occidArr = array();
-		$this->outputMsg('Indexing valid scientific names (e.g. populating tidinterpreted)... ',1);
-		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname WHERE o.collid IN('.$collId.') AND o.TidInterpreted IS NULL';
+		$sql = 'SELECT occid FROM omoccurrences WHERE family IS NOT NULL AND sciname IS NULL ';
+		if($this->collidStr) $sql .= 'AND collid IN('.$this->collidStr.')';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
 			$occidArr[] = $r->occid;
 			if(count($occidArr) > 1000){
-				$this->batchUpdateTidInterpreted($occidArr);
+				$this->batchScinameWithFamily($occidArr);
 				unset($occidArr);
 				$occidArr = array();
 			}
 		}
 		$rs->free();
-		$this->batchUpdateTidInterpreted($occidArr);
+		$this->batchScinameWithFamily($occidArr);
 		unset($occidArr);
 
 		//Update NULL image tids with non-NULL occurrence tids
 		$occidArr = array();
-		if($this->verbose) $this->outputMsg('Updating and indexing occurrence images... ',1);
-		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN images i ON o.occid = i.occid WHERE o.collid IN('.$collId.') AND (i.tid IS NULL) AND (o.tidinterpreted IS NOT NULL)';
+		$this->outputMsg('Updating and indexing occurrence images... ',1);
+		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN images i ON o.occid = i.occid WHERE (i.tid IS NULL) AND (o.tidinterpreted IS NOT NULL) ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.')';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
 			$occidArr[] = $r->occid;
@@ -107,9 +72,9 @@ public function generalOccurrenceCleaning($collId){
 
 		//Update NULL families with taxstatus family values
 		$occidArr = array();
-		if($this->verbose) $this->outputMsg('Updating null families using taxonomic thesaurus... ',1);
-		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN taxstatus ts ON o.tidinterpreted = ts.tid '.
-			'WHERE o.collid IN('.$collId.') AND (ts.taxauthid = 1) AND (ts.family IS NOT NULL) AND (o.family IS NULL)';
+		$this->outputMsg('Updating null families using taxonomic thesaurus... ',1);
+		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN taxstatus ts ON o.tidinterpreted = ts.tid WHERE (ts.taxauthid = 1) AND (ts.family IS NOT NULL) AND (o.family IS NULL)';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.')';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
 			$occidArr[] = $r->occid;
@@ -126,8 +91,8 @@ public function generalOccurrenceCleaning($collId){
 		//Updating records with null author
 		$occidArr = array();
 		$this->outputMsg('Updating null scientific authors using taxonomic thesaurus... ',1);
-		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN taxa t ON o.tidinterpreted = t.tid '.
-			'WHERE o.scientificNameAuthorship IS NULL AND t.author IS NOT NULL AND o.collid IN('.$collId.')';
+		$sql = 'SELECT o.occid FROM omoccurrences o INNER JOIN taxa t ON o.tidinterpreted = t.tid WHERE o.scientificNameAuthorship IS NULL AND t.author IS NOT NULL ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.')';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
 			$occidArr[] = $r->occid;
@@ -139,37 +104,93 @@ public function generalOccurrenceCleaning($collId){
 		$rs->free();
 		if(isset($occidArr)) $this->batchUpdateAuthor($occidArr);
 
-		/*
-		if($this->verbose) $this->outputMsg('Updating georeference index... ',1);
-		$sql = 'INSERT IGNORE INTO omoccurgeoindex(tid,decimallatitude,decimallongitude)
-			SELECT DISTINCT o.tidinterpreted, round(o.decimallatitude,2), round(o.decimallongitude,2)
-			FROM omoccurrences o
-			WHERE (o.tidinterpreted IS NOT NULL) AND (o.decimallatitude between -90 and 90) AND (o.decimallongitude between -180 and 180)
-			AND (o.cultivationStatus IS NULL OR o.cultivationStatus = 0) AND (o.coordinateUncertaintyInMeters IS NULL OR o.coordinateUncertaintyInMeters < 10000) ';
-		if(!$this->conn->query($sql)){
-			$errStr = 'WARNING: unable to update georeference index; '.$this->conn->error;
-			$this->errorArr[] = $errStr;
-			if($this->verbose) $this->outputMsg($errStr,2);
-			$status = false;
+		return $status;
+	}
+
+	public function indexOccurrencesToTaxa(){
+		$this->outputMsg('Indexing validated scientific names (e.g. populating tidInterpreted)... ', 1);
+
+		//Avoid using straight UPDATE SQL since they will often lock omoccurrences table for a significant amount of time when database is large
+		$occidArr = array();
+		//Index based on matching sciname and author
+		$activeTid = 0;
+		$sql = 'SELECT t.tid, o.occid
+			FROM omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname AND o.scientificnameauthorship = t.author
+			WHERE (o.TidInterpreted IS NULL) ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.') ';
+		$sql .= 'ORDER BY t.tid';
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_object()){
+			if($occidArr && $r->tid != $activeTid) $this->batchUpdateTidInterpreted($occidArr);
+			$activeTid = $r->tid;
+			$occidArr[$r->tid][] = $r->occid;
 		}
-		*/
+		$rs->free();
+		$this->batchUpdateTidInterpreted($occidArr);
 
-		return $status;
+		//Index base on matching sciname and family to improve correct match when cross kingdom homonyms exist
+		$activeTid = 0;
+		$sql = 'SELECT t.tid, o.occid
+			FROM omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname
+			INNER JOIN taxaenumtree e ON t.tid = e.tid
+			INNER JOIN taxa t2 ON e.parenttid = t2.tid
+			WHERE (o.TidInterpreted IS NULL) AND (t2.rankid = 140) AND (t2.sciname = o.family) ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.') ';
+		$sql .= 'ORDER BY t.tid';
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_object()){
+			if($occidArr && $r->tid != $activeTid) $this->batchUpdateTidInterpreted($occidArr);
+			$activeTid = $r->tid;
+			$occidArr[$r->tid][] = $r->occid;
+		}
+		$rs->free();
+		$this->batchUpdateTidInterpreted($occidArr);
+
+		//Update remaining taxa that can only be match on scientific name
+		$activeTid = 0;
+		$sql = 'SELECT t.tid, o.occid FROM omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname WHERE o.TidInterpreted IS NULL ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.') ';
+		$sql .= 'ORDER BY t.tid';
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_object()){
+			if($occidArr && $r->tid != $activeTid) $this->batchUpdateTidInterpreted($occidArr);
+			$activeTid = $r->tid;
+			$occidArr[$r->tid][] = $r->occid;
+		}
+		$rs->free();
+		$this->batchUpdateTidInterpreted($occidArr);
+
+		//Match subgeneric names
+		$activeTid = 0;
+		$sql = 'SELECT t.tid, o.occid
+			FROM omoccurrences o INNER JOIN taxa t ON CONCAT(SUBSTRING_INDEX(o.sciname, " (", 1), " ", SUBSTRING_INDEX(o.sciname, ") ", -1)) = t.sciname
+			WHERE o.tidinterpreted IS NULL AND o.sciname LIKE "% (%) %" ';
+		if($this->collidStr) $sql .= 'AND o.collid IN('.$this->collidStr.') ';
+		$sql .= 'ORDER BY t.tid';
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_object()){
+			if($occidArr && $r->tid != $activeTid) $this->batchUpdateTidInterpreted($occidArr);
+			$activeTid = $r->tid;
+			$occidArr[$r->tid][] = $r->occid;
+		}
+		$rs->free();
+		$this->batchUpdateTidInterpreted($occidArr);
 	}
 
-	private function batchUpdateTidInterpreted($occidArr){
+	private function batchUpdateTidInterpreted(&$occidArr){
 		$status = false;
-		if($occidArr){
-			$sql = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname SET o.TidInterpreted = t.tid WHERE o.occid IN('.implode(',',$occidArr).') ';
+		foreach($occidArr as $tid => $idArr){
+			$sql = 'UPDATE omoccurrences SET tidInterpreted = '.$tid.' WHERE occid IN('.implode(',',$idArr).') ';
 			if($this->conn->query($sql)){
 				$status = true;
 			}
 			else{
 				$this->errorArr[] = 'WARNING: unable to update tidinterpreted; '.$this->conn->error;
-				if($this->verbose) $this->outputMsg($this->errorArr,2);
+				$this->outputMsg($this->errorArr,2);
 				$status = false;
 			}
 		}
+		unset($occidArr);
 		return $status;
 	}
 
@@ -182,7 +203,23 @@ private function batchUpdateImageTid($occidArr){
 			}
 			else{
 				$this->errorArr[] = 'WARNING: unable to update image tid field; '.$this->conn->error;
-				if($this->verbose) $this->outputMsg($this->errorArr,2);
+				$this->outputMsg($this->errorArr,2);
+				$status = false;
+			}
+		}
+		return $status;
+	}
+
+	private function batchScinameWithFamily($occidArr){
+		$status = false;
+		if($occidArr){
+			$sql = 'UPDATE omoccurrences SET sciname = family WHERE occid IN('.implode(',',$occidArr).') ';
+			if($this->conn->query($sql)){
+				$status = true;
+			}
+			else{
+				$this->errorArr[] = 'WARNING: unable to update sciname using family; '.$this->conn->error;
+				$this->outputMsg($this->errorArr,2);
 				$status = false;
 			}
 		}
@@ -198,7 +235,7 @@ private function batchUpdateFamily($occidArr){
 			}
 			else{
 				$this->errorArr[] = 'WARNING: unable to update family in omoccurrence table; '.$this->conn->error;
-				if($this->verbose) $this->outputMsg($this->errorArr,2);
+				$this->outputMsg($this->errorArr,2);
 				$status = false;
 			}
 		}
@@ -214,25 +251,45 @@ private function batchUpdateAuthor($occidArr){
 			}
 			else{
 				$this->errorArr[] = 'WARNING: unable to update author; '.$this->conn->error;
-				if($this->verbose) $this->outputMsg($this->errorArr,2);
+				$this->outputMsg($this->errorArr,2);
 				$status = false;
 			}
 		}
 		return $status;
 	}
 
+	public function batchUpdateGeoreferenceIndex(){
+		$status = false;
+		$this->outputMsg('Updating georeference index... ',1);
+		$sql = 'INSERT IGNORE INTO omoccurgeoindex(tid,decimallatitude,decimallongitude)
+			SELECT DISTINCT o.tidinterpreted, round(o.decimallatitude,2), round(o.decimallongitude,2)
+			FROM omoccurrences o
+			WHERE (o.tidinterpreted IS NOT NULL) AND (o.decimallatitude between -90 and 90) AND (o.decimallongitude between -180 and 180)
+			AND (o.cultivationStatus IS NULL OR o.cultivationStatus = 0) AND (o.coordinateUncertaintyInMeters IS NULL OR o.coordinateUncertaintyInMeters < 10000) ';
+		if($this->conn->query($sql)){
+			$status = true;
+		}
+		else{
+			$errStr = 'WARNING: unable to update georeference index; '.$this->conn->error;
+			$this->errorArr[] = $errStr;
+			$this->outputMsg($errStr,2);
+		}
+		return $status;
+	}
+
+
 	//Protect Rare species data
-	public function protectRareSpecies($collid = 0){
+	public function protectRareSpecies(){
 		$status = 0;
-		$status = $this->protectGlobalSpecies($collid);
+		$status = $this->protectGlobalSpecies();
 		$status += $this->batchProtectStateRareSpecies();
 		return $status;
 	}
 
-	public function protectGlobalSpecies($collid = 0){
+	public function protectGlobalSpecies(){
 		$status = 0;
 		//protect globally rare species
-		if($this->verbose) $this->outputMsg('Protecting globally rare species... ',1);
+		$this->outputMsg('Protecting globally rare species... ',1);
 		//Only protect names on list and synonym of accepted names
 		$sensitiveArr = $this->getSensitiveTaxa();
 
@@ -240,14 +297,14 @@ public function protectGlobalSpecies($collid = 0){
 			$sql = 'UPDATE omoccurrences '.
 				'SET LocalitySecurity = 1 '.
 				'WHERE (LocalitySecurity IS NULL OR LocalitySecurity = 0) AND (localitySecurityReason IS NULL) AND (tidinterpreted IN('.implode(',',$sensitiveArr).')) ';
-			if($collid) $sql .= 'AND (collid = '.$collid.') ';
+			if($this->collidStr) $sql .= 'AND collid IN('.$this->collidStr.')';
 			if($this->conn->query($sql)){
 				$status += $this->conn->affected_rows;
 			}
 			else{
 				$errStr = 'WARNING: unable to protect globally rare species; '.$this->conn->error;
 				$this->errorArr[] = $errStr;
-				if($this->verbose) $this->outputMsg($errStr,2);
+				$this->outputMsg($errStr,2);
 				$status = false;
 			}
 		}
@@ -278,7 +335,7 @@ private function getSensitiveTaxa(){
 	public function batchProtectStateRareSpecies(){
 		$status = 0;
 		//Protect state level rare species
-		if($this->verbose) $this->outputMsg('Protecting state level rare species... ',1);
+		$this->outputMsg('Protecting state level rare species... ',1);
 		$sql = 'SELECT clid, locality FROM fmchecklists WHERE type = "rarespp"';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
@@ -310,7 +367,7 @@ public function protectStateRareSpecies($clid,$locality){
 			else{
 				$errStr = 'WARNING: unable to protect state level rare species; '.$this->conn->error;
 				$this->errorArr[] = $errStr;
-				if($this->verbose) $this->outputMsg($errStr,2);
+				$this->outputMsg($errStr,2);
 				$status = false;
 			}
 		}
@@ -336,165 +393,160 @@ public function getStateProtectionCount($clid, $state){
 	}
 
 	//Update statistics
-	public function updateCollectionStats($collid, $full = false){
-		set_time_limit(600);
-		$recordCnt = 0;
-		$georefCnt = 0;
-		$familyCnt = 0;
-		$genusCnt = 0;
-		$speciesCnt = 0;
-		if($full){
-			$statsArr = Array();
-			if($this->verbose) $this->outputMsg('Calculating specimen, georeference, family, genera, and species counts... ',1);
-			$sql = 'SELECT COUNT(o.occid) AS SpecimenCount, COUNT(o.decimalLatitude) AS GeorefCount, '.
-				'COUNT(DISTINCT o.family) AS FamilyCount, COUNT(o.typeStatus) AS TypeCount, '.
-				'COUNT(DISTINCT CASE WHEN t.RankId >= 180 THEN t.UnitName1 ELSE NULL END) AS GeneraCount, '.
-				'COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS SpecimensCountID, '.
-				'COUNT(DISTINCT CASE WHEN t.RankId = 220 THEN t.SciName ELSE NULL END) AS SpeciesCount, '.
-				'COUNT(DISTINCT CASE WHEN t.RankId >= 220 THEN t.SciName ELSE NULL END) AS TotalTaxaCount '.
-				'FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID '.
-				'WHERE (o.collid IN('.$collid.')) ';
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_object()){
-				$recordCnt = $r->SpecimenCount;
-				$georefCnt = $r->GeorefCount;
-				$familyCnt = $r->FamilyCount;
-				$genusCnt = $r->GeneraCount;
-				$speciesCnt = $r->SpeciesCount;
-				$statsArr['SpecimensCountID'] = $r->SpecimensCountID;
-				$statsArr['TotalTaxaCount'] = $r->TotalTaxaCount;
-				$statsArr['TypeCount'] = $r->TypeCount;
-			}
-			$rs->free();
-
-			if($this->verbose) $this->outputMsg('Calculating number of specimens imaged... ',1);
-			$sql = 'SELECT count(DISTINCT o.occid) as imgspeccnt, count(DISTINCT i.imgid) AS imgcnt '.
-				'FROM omoccurrences o INNER JOIN images i ON o.occid = i.occid '.
-				'WHERE (o.collid IN('.$collid.')) ';
-			$rs = $this->conn->query($sql);
-			if($r = $rs->fetch_object()){
-				$statsArr['imgcnt'] = $r->imgcnt.':'.$r->imgspeccnt;
-			}
-			$rs->free();
-
-			if($this->verbose) $this->outputMsg('Calculating genetic resources counts... ',1);
-			$sql = 'SELECT COUNT(CASE WHEN g.resourceurl LIKE "%boldsystems%" THEN o.occid ELSE NULL END) AS boldcnt, '.
-				'COUNT(CASE WHEN g.resourceurl LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS gencnt, '.
-				'COUNT(CASE WHEN g.resourceurl NOT LIKE "%boldsystems%" AND g.resourceurl NOT LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS geneticcnt '.
-				'FROM omoccurrences o INNER JOIN omoccurgenetic g ON o.occid = g.occid '.
-				'WHERE (o.collid IN('.$collid.')) ';
-			$rs = $this->conn->query($sql);
-			if($r = $rs->fetch_object()){
-				$statsArr['boldcnt'] = $r->boldcnt;
-				$statsArr['gencnt'] = $r->gencnt;
-				$statsArr['geneticcnt'] = $r->geneticcnt;
-			}
-			$rs->free();
-
-			if($this->verbose) $this->outputMsg('Calculating reference counts... ',1);
-			$sql = 'SELECT count(r.occid) as refcnt '.
-				'FROM omoccurrences o INNER JOIN referenceoccurlink r ON o.occid = r.occid '.
-				'WHERE (o.collid IN('.$collid.')) ';
-			$rs = $this->conn->query($sql);
-			if($r = $rs->fetch_object()){
-				$statsArr['refcnt'] = $r->refcnt;
-			}
-			$rs->free();
-
-			if($this->verbose) $this->outputMsg('Calculating counts per family... ',1);
-			$sql = 'SELECT o.family, COUNT(o.occid) AS SpecimensPerFamily, COUNT(o.decimalLatitude) AS GeorefSpecimensPerFamily, '.
-				'COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS IDSpecimensPerFamily, '.
-				'COUNT(CASE WHEN t.RankId >= 220 AND o.decimalLatitude IS NOT NULL THEN o.occid ELSE NULL END) AS IDGeorefSpecimensPerFamily '.
-				'FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID '.
-				'WHERE (o.collid IN('.$collid.')) '.
-				'GROUP BY o.family ';
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_object()){
-				$family = str_replace(array('"',"'"),"",$r->family);
-				if($family){
-					$statsArr['families'][$family]['SpecimensPerFamily'] = $r->SpecimensPerFamily;
-					$statsArr['families'][$family]['GeorefSpecimensPerFamily'] = $r->GeorefSpecimensPerFamily;
-					$statsArr['families'][$family]['IDSpecimensPerFamily'] = $r->IDSpecimensPerFamily;
-					$statsArr['families'][$family]['IDGeorefSpecimensPerFamily'] = $r->IDGeorefSpecimensPerFamily;
-				}
-			}
-			$rs->free();
-
-			if($this->verbose) $this->outputMsg('Calculating counts per country... ',1);
-			$sql = 'SELECT o.country, COUNT(o.occid) AS CountryCount, COUNT(o.decimalLatitude) AS GeorefSpecimensPerCountry, '.
-				'COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS IDSpecimensPerCountry, '.
-				'COUNT(CASE WHEN t.RankId >= 220 AND o.decimalLatitude IS NOT NULL THEN o.occid ELSE NULL END) AS IDGeorefSpecimensPerCountry '.
-				'FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID '.
-				'WHERE (o.collid IN('.$collid.')) '.
-				'GROUP BY o.country ';
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_object()){
-				$country = str_replace(array('"',"'"),"",$r->country);
-				if($country){
-					$statsArr['countries'][$country]['CountryCount'] = $r->CountryCount;
-					$statsArr['countries'][$country]['GeorefSpecimensPerCountry'] = $r->GeorefSpecimensPerCountry;
-					$statsArr['countries'][$country]['IDSpecimensPerCountry'] = $r->IDSpecimensPerCountry;
-					$statsArr['countries'][$country]['IDGeorefSpecimensPerCountry'] = $r->IDGeorefSpecimensPerCountry;
+	public function updateCollectionStatsFull(){
+		if($this->collidStr){
+			set_time_limit(600);
+			$collArr = explode(',', $this->collidStr);
+			foreach($collArr as $collid){
+				if(is_numeric($collid)){
+					$statsArr = Array();
+					$this->outputMsg('Calculating specimen, georeference, family, genera, and species counts... ', 1);
+					$sql = 'SELECT COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS SpecimensCountID,
+						COUNT(DISTINCT CASE WHEN t.RankId >= 220 THEN t.SciName ELSE NULL END) AS TotalTaxaCount, COUNT(o.typeStatus) AS TypeCount
+						FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID
+						WHERE o.collid IN('.$collid.')';
+					$rs = $this->conn->query($sql);
+					while($r = $rs->fetch_object()){
+						$statsArr['SpecimensCountID'] = $r->SpecimensCountID;
+						$statsArr['TotalTaxaCount'] = $r->TotalTaxaCount;
+						$statsArr['TypeCount'] = $r->TypeCount;
+					}
+					$rs->free();
+
+					$this->outputMsg('Calculating number of specimens imaged... ', 1);
+					$sql = 'SELECT count(DISTINCT o.occid) as imgspeccnt, count(DISTINCT i.imgid) AS imgcnt
+						FROM omoccurrences o INNER JOIN images i ON o.occid = i.occid
+						WHERE o.collid = '.$collid;
+					$rs = $this->conn->query($sql);
+					if($r = $rs->fetch_object()){
+						$statsArr['imgcnt'] = $r->imgcnt.':'.$r->imgspeccnt;
+					}
+					$rs->free();
+
+					$this->outputMsg('Calculating genetic resources counts... ', 1);
+					$sql = 'SELECT COUNT(CASE WHEN g.resourceurl LIKE "%boldsystems%" THEN o.occid ELSE NULL END) AS boldcnt,
+						COUNT(CASE WHEN g.resourceurl LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS gencnt,
+						COUNT(CASE WHEN g.resourceurl NOT LIKE "%boldsystems%" AND g.resourceurl NOT LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS geneticcnt
+						FROM omoccurrences o INNER JOIN omoccurgenetic g ON o.occid = g.occid
+						WHERE o.collid = '.$collid;
+					$rs = $this->conn->query($sql);
+					if($r = $rs->fetch_object()){
+						$statsArr['boldcnt'] = $r->boldcnt;
+						$statsArr['gencnt'] = $r->gencnt;
+						$statsArr['geneticcnt'] = $r->geneticcnt;
+					}
+					$rs->free();
+
+					$this->outputMsg('Calculating reference counts... ', 1);
+					$sql = 'SELECT count(r.occid) as refcnt FROM omoccurrences o INNER JOIN referenceoccurlink r ON o.occid = r.occid WHERE o.collid = '.$collid;
+					$rs = $this->conn->query($sql);
+					if($r = $rs->fetch_object()){
+						$statsArr['refcnt'] = $r->refcnt;
+					}
+					$rs->free();
+
+					$this->outputMsg('Calculating counts per family... ', 1);
+					$sql = 'SELECT o.family, COUNT(o.occid) AS SpecimensPerFamily, COUNT(o.decimalLatitude) AS GeorefSpecimensPerFamily,
+						COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS IDSpecimensPerFamily,
+						COUNT(CASE WHEN t.RankId >= 220 AND o.decimalLatitude IS NOT NULL THEN o.occid ELSE NULL END) AS IDGeorefSpecimensPerFamily
+						FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID
+						WHERE o.collid = '.$collid.' GROUP BY o.family ';
+					$rs = $this->conn->query($sql);
+					while($r = $rs->fetch_object()){
+						$family = str_replace(array('"',"'"),"",$r->family);
+						if($family){
+							$statsArr['families'][$family]['SpecimensPerFamily'] = $r->SpecimensPerFamily;
+							$statsArr['families'][$family]['GeorefSpecimensPerFamily'] = $r->GeorefSpecimensPerFamily;
+							$statsArr['families'][$family]['IDSpecimensPerFamily'] = $r->IDSpecimensPerFamily;
+							$statsArr['families'][$family]['IDGeorefSpecimensPerFamily'] = $r->IDGeorefSpecimensPerFamily;
+						}
+					}
+					$rs->free();
+
+					$this->outputMsg('Calculating counts per country... ', 1);
+					$sql = 'SELECT o.country, COUNT(o.occid) AS CountryCount, COUNT(o.decimalLatitude) AS GeorefSpecimensPerCountry,
+						COUNT(CASE WHEN t.RankId >= 220 THEN o.occid ELSE NULL END) AS IDSpecimensPerCountry,
+						COUNT(CASE WHEN t.RankId >= 220 AND o.decimalLatitude IS NOT NULL THEN o.occid ELSE NULL END) AS IDGeorefSpecimensPerCountry
+						FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID
+						WHERE o.collid = '.$collid.' GROUP BY o.country ';
+					$rs = $this->conn->query($sql);
+					while($r = $rs->fetch_object()){
+						$country = str_replace(array('"',"'"),"",$r->country);
+						if($country){
+							$statsArr['countries'][$country]['CountryCount'] = $r->CountryCount;
+							$statsArr['countries'][$country]['GeorefSpecimensPerCountry'] = $r->GeorefSpecimensPerCountry;
+							$statsArr['countries'][$country]['IDSpecimensPerCountry'] = $r->IDSpecimensPerCountry;
+							$statsArr['countries'][$country]['IDGeorefSpecimensPerCountry'] = $r->IDGeorefSpecimensPerCountry;
+						}
+					}
+					$rs->free();
+
+					if($statsArr) $this->updateCollectionStats(array('dynamicProperties' => json_encode($statsArr)), $collid);
+					$this->updateCollectionStatsBasic($collid);
 				}
 			}
-			$rs->free();
-
-			$returnArrJson = json_encode($statsArr);
-			$sql = 'UPDATE omcollectionstats '.
-				"SET dynamicProperties = '".$this->cleanInStr($returnArrJson)."' ".
-				'WHERE collid IN('.$collid.') ';
-			if(!$this->conn->query($sql)){
-				$errStr = 'WARNING: unable to update collection stats table [1]; '.$this->conn->error;
-				$this->errorArr[] = $errStr;
-				if($this->verbose) $this->outputMsg($errStr,2);
-			}
 		}
-		else{
-			if($this->verbose) $this->outputMsg('Calculating specimen, georeference, family, genera, and species counts... ',1);
+	}
+
+	public function updateCollectionStatsBasic($collid){
+		if(is_numeric($collid)){
+			$this->outputMsg('Calculating specimen, georeference, family, genera, and species counts... ',1);
+			$statArr = array();
 			$sql = 'SELECT COUNT(o.occid) AS SpecimenCount, COUNT(o.decimalLatitude) AS GeorefCount, COUNT(DISTINCT o.family) AS FamilyCount, '.
 				'COUNT(DISTINCT CASE WHEN t.RankId >= 180 THEN t.UnitName1 ELSE NULL END) AS GeneraCount, '.
 				'COUNT(DISTINCT CASE WHEN t.RankId = 220 THEN t.SciName ELSE NULL END) AS SpeciesCount '.
 				'FROM omoccurrences o LEFT JOIN taxa t ON o.tidinterpreted = t.TID '.
-				'WHERE (o.collid IN('.$collid.')) ';
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_object()){
-				$recordCnt = $r->SpecimenCount;
-				$georefCnt = $r->GeorefCount;
-				$familyCnt = $r->FamilyCount;
-				$genusCnt = $r->GeneraCount;
-				$speciesCnt = $r->SpeciesCount;
+				'WHERE o.collid = ?';
+			if($stmt = $this->conn->prepare($sql)){
+				$stmt->bind_param('i', $collid);
+				$stmt->execute();
+				$stmt->bind_result($recCnt, $georefCnt, $familyCnt, $genusCnt, $speciesCnt);
+				if($stmt->fetch()){
+					$statArr['recordcnt'] = $recCnt;
+					$statArr['georefcnt'] = $georefCnt;
+					$statArr['familycnt'] = $familyCnt;
+					$statArr['genuscnt'] = $genusCnt;
+					$statArr['speciescnt'] =  $speciesCnt;
+				}
+				$stmt->close();
 			}
-		}
-
-		$sql = 'UPDATE omcollectionstats cs '.
-			'SET cs.recordcnt = '.$recordCnt.',cs.georefcnt = '.$georefCnt.',cs.familycnt = '.$familyCnt.',cs.genuscnt = '.$genusCnt.
-			',cs.speciescnt = '.$speciesCnt.', cs.datelastmodified = CURDATE() '.
-			'WHERE cs.collid IN('.$collid.')';
-		if(!$this->conn->query($sql)){
-			$errStr = 'WARNING: unable to update collection stats table [2]; '.$this->conn->error;
-			$this->errorArr[] = $errStr;
-			if($this->verbose) $this->outputMsg($errStr,2);
+			if($statArr) $this->updateCollectionStats($statArr, $collid);
 		}
 	}
 
-	//Misc support functions
-	public function getCollectionMetadata($collid){
-		$retArr = array();
-		if(is_numeric($collid)){
-			$sql = 'SELECT institutioncode, collectioncode, collectionname, colltype, managementtype '.
-				'FROM omcollections '.
-				'WHERE collid = '.$collid;
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_object()){
-				$retArr['instcode'] = $r->institutioncode;
-				$retArr['collcode'] = $r->collectioncode;
-				$retArr['collname'] = $r->collectionname;
-				$retArr['colltype'] = $r->colltype;
-				$retArr['mantype'] = $r->managementtype;
+	private function updateCollectionStats($inputData, $collid){
+		$status = false;
+		if($inputData){
+			$paramArr = array();
+			$type = '';
+			$sql = 'UPDATE omcollectionstats SET ';
+			foreach($inputData as $field => $value){
+				$sql .= $field.' = ?, ';
+				if($field == 'dynamicProperties') $type .= 's';
+				else $type .= 'i';
+				$paramArr[] = $value;
+			}
+			$sql .= ' datelastmodified = NOW() WHERE collid = ?';
+			$type .= 'i';
+			$paramArr[] = $collid;
+			if($stmt = $this->conn->prepare($sql)){
+				$stmt->bind_param($type, ...$paramArr);
+				$stmt->execute();
+				if($stmt->error){
+					$errStr = 'ERROR updating collection stats table: '.$stmt->error;
+					$this->errorArr[] = $errStr;
+					$this->outputMsg($errStr,2);
+				}
+				else $status = true;
+				$stmt->close();
 			}
-			$rs->free();
 		}
-		return $retArr;
+		return $status;
+	}
+
+	//Setters and getters
+	public function setCollidStr($idStr){
+		if($idStr && preg_match('/^[\d,]+$/', $idStr)) $this->collidStr = $idStr;
 	}
 
 	public function setVerbose($v){
@@ -510,17 +562,13 @@ public function getErrorArr(){
 		return $this->errorArr;
 	}
 
+	//Misc support functions
 	private function outputMsg($str, $indent = 0){
-		if($this->verbose) echo '<li style="margin-left:'.($indent*10).'px;">'.$str.'</li>';
-		ob_flush();
-		flush();
-	}
-
-	private function cleanInStr($inStr){
-		$retStr = trim($inStr);
-		$retStr = preg_replace('/\s\s+/', ' ',$retStr);
-		$retStr = $this->conn->real_escape_string($retStr);
-		return $retStr;
+		if($this->verbose){
+			echo '<li style="margin-left:'.($indent*15).'px;">'.$str.'</li>';
+			ob_flush();
+			flush();
+		}
 	}
 }
 ?>
\ No newline at end of file
diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
index d60340ddf1..d5b6e2f070 100644
--- a/classes/SpecUploadBase.php
+++ b/classes/SpecUploadBase.php
@@ -1499,8 +1499,9 @@ protected function finalCleanup(){
 
 		//Do some more cleaning of the data after it has been indexed in the omoccurrences table
 		$occurMain = new OccurrenceMaintenance($this->conn);
+		$occurMain->setCollidStr($this->collId);
 
-		if(!$occurMain->generalOccurrenceCleaning($this->collId)){
+		if(!$occurMain->generalOccurrenceCleaning()){
 			$errorArr = $occurMain->getErrorArr();
 			foreach($errorArr as $errorStr){
 				$this->outputMsg('<li style="margin-left:20px;">'.$errorStr.'</li>',1);
@@ -1508,10 +1509,10 @@ protected function finalCleanup(){
 		}
 
 		$this->outputMsg('<li style="margin-left:10px;">Protecting sensitive species...</li>');
-		$protectCnt = $occurMain->protectRareSpecies($this->collId);
+		$protectCnt = $occurMain->protectRareSpecies();
 
 		$this->outputMsg('<li style="margin-left:10px;">Updating statistics...</li>');
-		if(!$occurMain->updateCollectionStats($this->collId)){
+		if(!$occurMain->updateCollectionStatsFull()){
 			$errorArr = $occurMain->getErrorArr();
 			foreach($errorArr as $errorStr){
 				$this->outputMsg('<li style="margin-left:20px;">'.$errorStr.'</li>',1);
diff --git a/classes/TPDescEditorManager.php b/classes/TPDescEditorManager.php
index c4817196af..800a1726a7 100644
--- a/classes/TPDescEditorManager.php
+++ b/classes/TPDescEditorManager.php
@@ -14,8 +14,8 @@ public function __destruct(){
 	public function getDescriptions(){
 		$descrArr = Array();
 		$langArr = false;
-		$sql = 'SELECT p.tdProfileID, IFNULL(p.caption, d.caption) as caption, IFNULL(p.publication, d.source) AS source, IFNULL(p.urlTemplate, d.sourceurl) AS sourceurl,
-			IFNULL(p.defaultDisplayLevel, d.displaylevel) AS displaylevel, t.tid, t.sciname, d.tdbid, d.notes, l.langid, d.language
+		$sql = 'SELECT p.tdProfileID, IFNULL(d.caption, p.caption) as caption, IFNULL(d.source, p.publication) AS source, IFNULL(d.sourceurl, p.urlTemplate) AS sourceurl,
+			IFNULL(d.displaylevel, p.defaultDisplayLevel) AS displaylevel, t.tid, t.sciname, d.tdbid, d.notes, l.langid, d.language
 			FROM taxadescrprofile p INNER JOIN taxadescrblock d ON p.tdProfileID = d.tdProfileID
 			LEFT JOIN adminlanguages l ON p.langid = l.langid ';
 		if($this->acceptance){
diff --git a/classes/TaxonProfile.php b/classes/TaxonProfile.php
index efbb9d9b0c..b2d02f4869 100644
--- a/classes/TaxonProfile.php
+++ b/classes/TaxonProfile.php
@@ -340,8 +340,8 @@ private function getDescriptions(){
 		$retArr = Array();
 		if($this->tid){
 			$rsArr = array();
-			$sql = 'SELECT p.tdProfileID, IFNULL(p.caption, d.caption) as caption, IFNULL(p.publication, d.source) AS source, IFNULL(p.urlTemplate, d.sourceurl) AS sourceurl,
-				IFNULL(p.defaultDisplayLevel, d.displaylevel) AS displaylevel, d.tid, d.tdbid, s.tdsid, s.heading, s.statement, s.displayheader, d.language, p.langid
+			$sql = 'SELECT p.tdProfileID, IFNULL(d.caption, p.caption) as caption, IFNULL(d.source, p.publication) AS source, IFNULL(d.sourceurl, p.urlTemplate) AS sourceurl,
+				IFNULL(d.displaylevel, p.defaultDisplayLevel) AS displaylevel, d.tid, d.tdbid, s.tdsid, s.heading, s.statement, s.displayheader, d.language, p.langid
 				FROM taxadescrprofile p INNER JOIN taxadescrblock d ON p.tdProfileID = d.tdProfileID
 				INNER JOIN taxadescrstmts s ON d.tdbid = s.tdbid
 				LEFT JOIN adminlanguages l ON p.langid = l.langid ';
@@ -482,6 +482,23 @@ public function getLinkArr(){
 		return $this->linkArr;
 	}
 
+	public function getResourceLinkArr(){
+		$retArr = array();
+		if($this->tid){
+			$sql = 'SELECT taxaResourceID, sourceName, sourceIdentifier, sourceGuid, url, notes FROM taxaresourcelinks WHERE tid = '.$this->tid.' ORDER BY ranking, sourceName';
+			$rs = $this->conn->query($sql);
+			while($r = $rs->fetch_object()){
+				$retArr[$r->taxaResourceID]['name'] = $r->sourceName;
+				$retArr[$r->taxaResourceID]['id'] = $r->sourceIdentifier;
+				$retArr[$r->taxaResourceID]['guid'] = $r->sourceGuid;
+				$retArr[$r->taxaResourceID]['url'] = $r->url;
+				$retArr[$r->taxaResourceID]['notes'] = $r->notes;
+			}
+			$rs->free();
+		}
+		return $retArr;
+	}
+
 	//Set children data for taxon higher than species level
 	public function getSppArray($page, $taxaLimit, $pid, $clid){
 		if(!$this->sppArray && $this->tid){
diff --git a/classes/TaxonomyCleaner.php b/classes/TaxonomyCleaner.php
index e824d19c33..0bf44d0328 100644
--- a/classes/TaxonomyCleaner.php
+++ b/classes/TaxonomyCleaner.php
@@ -3,6 +3,7 @@
 include_once($SERVER_ROOT.'/classes/Manager.php');
 include_once($SERVER_ROOT.'/classes/TaxonomyUtilities.php');
 include_once($SERVER_ROOT.'/classes/TaxonomyHarvester.php');
+include_once($SERVER_ROOT.'/classes/OccurrenceMaintenance.php');
 
 class TaxonomyCleaner extends Manager{
 
@@ -306,42 +307,10 @@ private function indexOccurrenceTaxa(){
 		flush();
 		ob_flush();
 
-		$sql = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname '.
-			'SET o.tidinterpreted = t.tid '.
-			'WHERE (o.collid IN('.$this->collid.')) AND (o.tidinterpreted IS NULL) ';
-		//echo $sql;
-		if($this->conn->query($sql)){
-			$this->logOrEcho('Indexing names based on exact matches... ' . $this->conn->affected_rows.' occurrence records mapped', 1);
-		}
-		else{
-			$this->logOrEcho('ERROR linking new data to occurrences: '.$this->conn->error, 1);
-		}
-		flush();
-		ob_flush();
-
-		$sql = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.tidinterpreted = t.tid
-			SET o.scientificNameAuthorship = t.author
-			WHERE (o.collid IN('.$this->collid.')) AND (o.scientificNameAuthorship IS NULL) AND (t.author IS NOT NULL) ';
-		if($this->conn->query($sql)){
-			$this->logOrEcho('Populating null scientific authors within occurrence tables... ' . $this->conn->affected_rows.' occurrence records populated', 1);
-		}
-		else{
-			$this->logOrEcho('ERROR updating authors: '.$this->conn->error, 1);
-		}
-		flush();
-		ob_flush();
-
-		$sql = 'UPDATE omoccurrences o INNER JOIN taxstatus ts ON o.tidinterpreted = ts.tid
-			SET o.family = ts.family
-			WHERE (o.collid IN('.$this->collid.')) AND (o.family IS NULL) AND (ts.family IS NOT NULL) ';
-		if($this->conn->query($sql)){
-			$this->logOrEcho('Populating null family names within occurrence tables... ' . $this->conn->affected_rows . ' occurrence records populated', 1);
-		}
-		else{
-			$this->logOrEcho('ERROR updating family occurrences: '.$this->conn->error, 1);
-		}
-		flush();
-		ob_flush();
+		$occurMaintenance = new OccurrenceMaintenance($this->conn);
+		$occurMaintenance->setCollidStr($this->collid);
+		$occurMaintenance->setVerbose(true);
+		$occurMaintenance->generalOccurrenceCleaning();
 	}
 
 	public function remapOccurrenceTaxon($collid, $oldSciname, $tid, $idQualifier = ''){
diff --git a/classes/TaxonomyCleanerOccurrences.php b/classes/TaxonomyCleanerOccurrences.php
index b006988f0b..4def13c06d 100644
--- a/classes/TaxonomyCleanerOccurrences.php
+++ b/classes/TaxonomyCleanerOccurrences.php
@@ -1,10 +1,10 @@
 <?php
 include_once($SERVER_ROOT.'/config/dbconnection.php');
-  
+
 class TaxonomyCleanerOccurrences extends TaxonomyCleaner{
 
 	private $collId;
-	
+
 	public function __construct(){
  		parent::__construct();
 	}
@@ -13,22 +13,13 @@ function __destruct(){
  		parent::__destruct();
 	}
 
-	public function linkSciNames($collId){
-		//First make sure that all tidinterpreted have been checked 
-		$sql = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname '.
-			'SET o.tidinterpreted = t.tid '.
-			'WHERE o.tidinterpreted IS NULL ';
-		if($collId && is_numeric($collId)) $sql .= 'AND (o.collid = '.$collId.')';
-		$this->conn->query($sql);
-	}
-
 	public function verifyCollectionTaxa($collId){
 		//Grab list of taxa, check each one, add valid taxa to taxonomic thesaurus, return number added and number problematic remaining
 		$numGood = 0;
 		$numBad = 0;
 		$sql = 'SELECT DISTINCT o.sciname FROM omoccurrences o '.
 			'WHERE o.tidinterpreted IS NULL AND o.sciname IS NOT NULL ';
-		if($collId && is_numeric($collId)) $sql .= 'AND (o.collid = '.$collId.') '; 
+		if($collId && is_numeric($collId)) $sql .= 'AND (o.collid = '.$collId.') ';
 		$sql .= 'ORDER BY o.sciname LIMIT 1';
 		//echo '<div>'.$sql.'</div>';
 		$rs = $this->conn->query($sql);
@@ -42,22 +33,22 @@ public function verifyCollectionTaxa($collId){
 						//Default to internal system's taxonomy
 							//1. Go through external synonyms
 							//2. If one is found and taxonomically tested, add new name linked to the accepted name of that taxon
-							//3. Add and link rest of the Synonyms to this name 
+							//3. Add and link rest of the Synonyms to this name
 						//Default to external system's taxonomy
 							//1. Add name as accepted
 							//2. Go through synonyms and add linked to new name
-							//3. If synonym already exists, link to accetped name 
+							//3. If synonym already exists, link to accetped name
 					//External is not accepted
 						//1. Grab and test external accepted name
 						//Default to internal system's taxonomy
-							//2a. Accepted name does not exist: Go through synonyms and test, 
+							//2a. Accepted name does not exist: Go through synonyms and test,
 								//3a. If one exists, map all to this accepted taxon
 								//3b. If not, add accepted name and link all to it (including synonyms)
-							//2b. Accepted name exists: Link all to it (including synonyms) 
+							//2b. Accepted name exists: Link all to it (including synonyms)
 						//Default to external system's taxonomy
 							//4a. External accepted does not exist: add name and link all to it (including synonyms that don't exist)
 							//4b. External accepted does exists...
-								
+
 				}
 				else{
 					//Name is not good, mark as so
@@ -95,7 +86,7 @@ private function getHierarchy($tid){
 			if($targetTid == $parentTid) break;
 			$targetTid = $parentTid;
 		}while($targetTid && $parCnt < 16);
-		
+
 		return implode(",",array_reverse($parentArr));
 	}
 
@@ -112,7 +103,7 @@ public function getCollectionName(){
 		}
 		return $retStr;
 	}
-	
+
 	public function getTaxaList($index = 0){
 		$retArr = array();
 		$sql = 'SELECT sciname '.
@@ -128,7 +119,7 @@ public function getTaxaList($index = 0){
 		}
 		return $retArr;
 	}
-	
+
 	public function analyzeTaxa($startIndex = 0, $limit = 10){
 		$retArr = array();
 		$sql = 'SELECT sciname '.
@@ -141,11 +132,11 @@ public function analyzeTaxa($startIndex = 0, $limit = 10){
 				$sn = $row->sciname;
 				$sxArr[$sn] = $sn;
 				//Check name through Catalog of Life
-				
+
 				//Check for near match using SoundEx
 				$sxArr = $this->getSoundexMatch($sn);
 				if($sxArr) $retArr[$sn]['soundex'] = $sxArr;
-				
+
 			}
 			$rs->close();
 		}
@@ -167,7 +158,7 @@ public function getTaxaCount(){
 		}
 		return $retStr;
 	}
-	
+
 	public function setCollId($id){
 		if(is_numeric($id)){
 			$this->collId = $id;
diff --git a/classes/TaxonomyHarvester.php b/classes/TaxonomyHarvester.php
index 4cf66c7bd6..296b6073a3 100644
--- a/classes/TaxonomyHarvester.php
+++ b/classes/TaxonomyHarvester.php
@@ -137,9 +137,13 @@ private function addSciname($taxonArr, $resourceKey){
 	 */
 	private function addColTaxon($taxonArr){
 		$tid = 0;
+		if(preg_match('/^[A-Z){1}[a-z]+\s{1}\(([A-Z){1}[a-z]+)\)$/', $taxonArr['sciname'], $m)){
+			//Remove Genus from subgeneric name
+			$taxonArr['sciname'] = $m[1];
+		}
 		$sciName = $taxonArr['sciname'];
 		if($sciName){
-			//$url = 'https://api.catalogueoflife.org/nameusage/search?content=SCIENTIFIC_NAME&q='.str_replace(' ','%20'.,$adjustedName).'&offset=0&limit=10';
+			//$url = 'https://api.catalogueoflife.org/nameusage/search?content=SCIENTIFIC_NAME&q='.str_replace(' ','%20',$sciName).'&offset=0&limit=10';
 			$url = 'https://webservice.catalogueoflife.org/col/webservice?response=full&format=json&name='.str_replace(' ','%20',$sciName);
 			//echo $url.'<br/>';
 			$retArr = $this->getContentString($url);
@@ -147,16 +151,16 @@ private function addColTaxon($taxonArr){
 			$resultArr = json_decode($content,true);
 			$numResults = $resultArr['number_of_results_returned'];
 			if($numResults){
+				//Evaluate and rank each result to determine which is the best suited target
 				$adjustedName = $sciName;
 				if(isset($taxonArr['rankid']) && $taxonArr['rankid'] > 220) $adjustedName = trim($taxonArr['unitname1'].' '.$taxonArr['unitname2'].' '.$taxonArr['unitname3']);
 				$targetKey = 0;
 				$submitArr = array();
-				$rankArr = array();
+				$rankingArr = array();
 				foreach($resultArr['result'] as $k => $tArr){
-					//Evaluate and rank each result to determine which is the best suited target
-					$rankArr[$k] = 0;
+					$rankingArr[$k] = 0;
 					if($sciName != $tArr['name'] && $adjustedName != $tArr['name']){
-						unset($rankArr[$k]);
+						unset($rankingArr[$k]);
 						continue;
 					}
 					$this->setColClassification($tArr,$taxonArr);
@@ -164,7 +168,7 @@ private function addColTaxon($taxonArr){
 					$taxonKingdom = $this->getColParent($tArr, 'Kingdom');
 					if($this->kingdomName && $taxonKingdom && $this->kingdomName != $taxonKingdom){
 						//Skip if kingdom doesn't match target kingdom
-						unset($rankArr[$k]);
+						unset($rankingArr[$k]);
 						$msg = $sciName;
 						$id = '';
 						if(isset($resultArr['result'][$k]['id'])){
@@ -177,15 +181,16 @@ private function addColTaxon($taxonArr){
 					}
 					if($taxonArr['unitind3'] && isset($tArr['infraspeciesMarker']) && $taxonArr['unitind3'] != $tArr['infraspeciesMarker']){
 						//Skip because it's not the correct infraspecific rank
-						unset($rankArr[$k]);
+						unset($rankingArr[$k]);
 						continue;
 					}
-					if($this->defaultFamily && $this->defaultFamily == $this->getColParent($tArr, 'Family')) $rankArr[$k] += 2;
-					if($tArr['name_status'] == 'accepted name')  $rankArr[$k] += 2;
+					if(isset($taxonArr['taxonRank']) && isset($tArr['rank']) && $taxonArr['taxonRank'] == $tArr['rank']) $rankingArr[$k] += 2;
+					if($this->defaultFamily && $this->defaultFamily == $this->getColParent($tArr, 'Family')) $rankingArr[$k] += 2;
+					if($tArr['name_status'] == 'accepted name')  $rankingArr[$k] += 2;
 					if(isset($tArr['author']) && $tArr['author']){
 						if(stripos($tArr['author'],'nom. illeg.') !== false){
 							//Skip if name is an illegal homonym
-							unset($rankArr[$k]);
+							unset($rankingArr[$k]);
 							continue;
 						}
 						//Gets 2 points if author is the same, 1 point if 80% similar
@@ -194,18 +199,29 @@ private function addColTaxon($taxonArr){
 							$author2 = str_replace(array(' ','.'), '', $tArr['author']);
 							$percent = 0;
 							similar_text($author1, $author2, $percent);
-							if($author1 == $author2) $rankArr[$k] += 2;
-							elseif($percent > 80) $rankArr[$k] += 1;
+							if($author1 == $author2) $rankingArr[$k] += 2;
+							elseif($percent > 80) $rankingArr[$k] += 1;
 						}
 					}
 					$submitArr[$k] = $resultArr['result'][$k];
 				}
-				if($rankArr){
-					asort($rankArr);
-					end($rankArr);
-					$targetKey = key($rankArr);
-					if(isset($rankArr[0]) && $rankArr[$targetKey] == $rankArr[0]) $targetKey = 0;
+				if($rankingArr){
+					asort($rankingArr);
+					end($rankingArr);
+					$targetKey = key($rankingArr);
+					if(isset($rankingArr[0]) && $rankingArr[$targetKey] == $rankingArr[0]) $targetKey = 0;
 				}
+				//If taxon has an accepted taxon that is the same taxon with a subgeneric linkage, use the taxon object to be submitted
+				if(isset($submitArr[$targetKey]['accepted_name'])){
+					if(preg_match('/^([A-Z]{1}[a-z]+)\s{1}\(\D+\)\s{1}([a-z .]+)/', $submitArr[$targetKey]['accepted_name']['name'], $m)){
+						$acceptedBaseName = $m[1].' '.$m[2];
+						if($submitArr[$targetKey]['name'] == $acceptedBaseName){
+							$submitArr[0] = $submitArr[$targetKey]['accepted_name'];
+							$targetKey = 0;
+						}
+					}
+				}
+				//Process selected result
 				$this->logOrEcho('<i>'.$sciName.'</i> found within Catalog of Life',2);
 				if(array_key_exists($targetKey, $submitArr) && $submitArr[$targetKey]){
 					$tid = $this->addColTaxonByResult($submitArr[$targetKey]);
@@ -222,7 +238,14 @@ private function addColTaxonByResult($baseArr){
 		$taxonArr = array();
 		if($baseArr){
 			$taxonArr = $this->translateColNode($baseArr);
-			$this->setColClassification($baseArr,$taxonArr);
+			$this->setColClassification($baseArr, $taxonArr);
+			if($taxonArr['rankid'] == 190){
+				if(!strpos($taxonArr['sciname'], ' (') && isset($baseArr['formattedClassification'][180]['sciname'])){
+					$reformattedName = $baseArr['formattedClassification'][180]['sciname'].' ('.$taxonArr['sciname'].')';
+					$taxonArr['sciname'] = $reformattedName;
+					$taxonArr['unitname1'] = $reformattedName;
+				}
+			}
 			if(isset($baseArr['formattedClassification'][140]['sciname'])) $taxonArr['family'] = $baseArr['formattedClassification'][140]['sciname'];
 			$tidAccepted = 0;
 			if($baseArr['name_status'] == 'synonym' && isset($baseArr['accepted_name'])){
@@ -276,75 +299,68 @@ private function addColTaxonByResult($baseArr){
 	}
 
 	private function addColTaxonById($taxonArr){
-	    $tid = 0;
-	    if($taxonArr['id']){
-	        $url = 'https://webservice.catalogueoflife.org/col/webservice?response=full&format=json&id='.$taxonArr['id'];
-	        //echo $url.'<br/>';
-	        $retArr = $this->getContentString($url);
-	        $content = $retArr['str'];
-	        $resultArr = json_decode($content,true);
-	        if(isset($resultArr['result'][0])){
-	            $baseArr = $resultArr['result'][0];
-	            if(isset($taxonArr['datasetKey'])) $baseArr['datasetKey'] = $taxonArr['datasetKey'];
-	            if(isset($taxonArr['formattedClassification'])) $baseArr['formattedClassification'] = $taxonArr['formattedClassification'];
-	            $tid = $this->addColTaxonByResult($baseArr);
-	        }
-	        else{
-	            $this->logOrEcho('Targeted taxon return does not exist(2)',2);
-	        }
-	    }
-	    else{
-	        $this->logOrEcho('ERROR harvesting COL name: null input identifier',1);
-	    }
-	    return $tid;
+		$tid = 0;
+		if($taxonArr['id']){
+			$url = 'https://webservice.catalogueoflife.org/col/webservice?response=full&format=json&id='.$taxonArr['id'];
+			$retArr = $this->getContentString($url);
+			$content = $retArr['str'];
+			$resultArr = json_decode($content,true);
+			if(isset($resultArr['result'][0])){
+				$baseArr = $resultArr['result'][0];
+				if(isset($taxonArr['datasetKey'])) $baseArr['datasetKey'] = $taxonArr['datasetKey'];
+				if(isset($taxonArr['formattedClassification'])) $baseArr['formattedClassification'] = $taxonArr['formattedClassification'];
+				$tid = $this->addColTaxonByResult($baseArr);
+			}
+			else{
+				$this->logOrEcho('Targeted taxon return does not exist(2)',2);
+			}
+		}
+		else{
+			$this->logOrEcho('ERROR harvesting COL name: null input identifier',1);
+		}
+		return $tid;
 	}
 
 	private function translateColNode($nodeArr){
+		//Translates COL output from v1 (webservices) or v2 (api) to a Symbiota taxon object
 		$taxonArr = array();
 		if(isset($nodeArr['id'])) $taxonArr['id'] = $nodeArr['id'];
 		if(isset($nodeArr['name'])) $taxonArr['sciname'] = $nodeArr['name'];
+		elseif(isset($nodeArr['name']['scientificName'])) $taxonArr['sciname'] = $nodeArr['name']['scientificName'];
 		if(isset($nodeArr['rank'])) $taxonArr['taxonRank'] = $nodeArr['rank'];
+		elseif(isset($nodeArr['name']['rank'])) $taxonArr['taxonRank'] = $nodeArr['name']['rank'];
 		if(isset($nodeArr['genus'])) $taxonArr['unitname1'] = $nodeArr['genus'];
+		elseif(isset($nodeArr['name']['genus'])) $taxonArr['unitname1'] = $nodeArr['name']['genus'];
+		elseif(isset($nodeArr['name']['uninomial'])) $taxonArr['unitname1'] = $nodeArr['name']['uninomial'];
 		if(isset($nodeArr['species'])) $taxonArr['unitname2'] = $nodeArr['species'];
+		elseif(isset($nodeArr['name']['specificEpithet'])) $taxonArr['unitname2'] = $nodeArr['name']['specificEpithet'];
 		if(isset($nodeArr['infraspecies'])) $taxonArr['unitname3'] = $nodeArr['infraspecies'];
+		elseif(isset($nodeArr['name']['infraSpecificEpithet'])) $taxonArr['unitname3'] = $nodeArr['name']['infraSpecificEpithet'];
 		if(isset($nodeArr['infraspeciesMarker'])){
 			$taxonArr['unitind3'] = $nodeArr['infraspeciesMarker'];
 			$taxonArr['sciname'] = trim($taxonArr['unitname1'].' '.$taxonArr['unitname2'].($taxonArr['unitind3']?' '.$taxonArr['unitind3']:'').' '.$taxonArr['unitname3']);
 		}
 		if(isset($nodeArr['author'])) $taxonArr['author'] = $nodeArr['author'];
+		elseif(isset($nodeArr['name']['authorship'])) $taxonArr['author'] = $nodeArr['name']['authorship'];
 		if(isset($nodeArr['source_database'])) $taxonArr['source'] = $nodeArr['source_database'];
-		if(isset($nodeArr['source_database_url'])) $taxonArr['sourceURL'] = $nodeArr['source_database_url'];
+		elseif(isset($nodeArr['datasetKey'])) $taxonArr['source'] = '<a href="https://www.catalogueoflife.org/data/dataset/'.$nodeArr['datasetKey'].'" target="_blank">https://www.catalogueoflife.org/data/dataset/'.$nodeArr['datasetKey'].'</a>';
+		if(isset($nodeArr['online_resource'])) $taxonArr['sourceURL'] = $nodeArr['online_resource'];
+		elseif(isset($nodeArr['link'])) $taxonArr['sourceURL'] = $nodeArr['link'];
+		if(isset($nodeArr['url'])) $taxonArr['resourceURL'] = $nodeArr['url'];
 		$rankID = $this->getRankIdByTaxonArr($taxonArr);
 		if($rankID){
 			$taxonArr['rankid'] = $rankID;
+			if($rankID > 190){
+				if(preg_match('/^([A-Z]{1}[a-z]+)\s{1}\(\D+\)\s{1}(.*)/', $taxonArr['sciname'], $m)){
+					$taxonArr['sciname'] = $m[1].' '.$m[2];
+				}
+			}
 			if(!isset($taxonArr['unitname1'])) $taxonArr = array_merge(TaxonomyUtilities::parseScientificName($taxonArr['sciname'],$this->conn,$taxonArr['rankid'],$this->kingdomName),$taxonArr);
 		}
 		//$this->buildTaxonArr($taxonArr);
 		return $taxonArr;
 	}
 
-	private function translateColApiNode($nodeArr){
-		$taxonArr = array();
-		if(isset($nodeArr['id'])) $taxonArr['id'] = $nodeArr['id'];
-		if(isset($nodeArr['name']['scientificName'])) $taxonArr['sciname'] = $nodeArr['name']['scientificName'];
-		if(isset($nodeArr['name']['rank'])) $taxonArr['taxonRank'] = $nodeArr['name']['rank'];
-		if(isset($nodeArr['name']['genus'])) $taxonArr['unitname1'] = $nodeArr['name']['genus'];
-		elseif(isset($nodeArr['name']['uninomial'])) $taxonArr['unitname1'] = $nodeArr['name']['uninomial'];
-		if(isset($nodeArr['name']['specificEpithet'])) $taxonArr['unitname2'] = $nodeArr['name']['specificEpithet'];
-		if(isset($nodeArr['name']['infraSpecificEpithet'])) $taxonArr['unitname3'] = $nodeArr['name']['infraSpecificEpithet'];
-		if(isset($nodeArr['name']['authorship'])) $taxonArr['author'] = $nodeArr['name']['authorship'];
-		if(isset($nodeArr['datasetKey'])) $taxonArr['source'] = '<a href="https://www.catalogueoflife.org/data/dataset/'.$nodeArr['datasetKey'].'" target="_blank">https://www.catalogueoflife.org/data/dataset/'.$nodeArr['datasetKey'].'</a>';
-		if(isset($nodeArr['link'])) $taxonArr['sourceURL'] = $nodeArr['link'];
-		$rankID = $this->getRankIdByTaxonArr($taxonArr);
-		if($rankID) $taxonArr['rankid'] = $rankID;
-		if(isset($taxonArr['unitname3']) && $taxonArr['unitname3'] && ($this->kingdomName == 'Plantae' || $this->kingdomName == 'Fungi')){
-			if($taxonArr['rankid'] == 230) $taxonArr['unitind3'] = 'subsp.';
-			if($taxonArr['rankid'] == 240) $taxonArr['unitind3'] = 'var.';
-			if($taxonArr['rankid'] == 260) $taxonArr['unitind3'] = 'f.';
-		}
-		return $taxonArr;
-	}
-
 	private function setColClassification(&$tArr, $subjectTaxonArr){
 		if(isset($tArr['formattedClassification'])) return true;
 		$classificationArr = array();
@@ -363,7 +379,7 @@ private function setColClassification(&$tArr, $subjectTaxonArr){
 				$resultArr = json_decode($content,true);
 				if(isset($resultArr['total']) && $resultArr['total']){
 					foreach($resultArr['result'] as $k => $rArr){
-						if($rArr['id'] == $tArr['id'] && isset($rArr['classification'])){
+						if(isset($rArr['id']) && $rArr['id'] == $tArr['id'] && isset($rArr['classification'])){
 							$activeClassArr = $rArr['classification'];
 							if(!isset($tArr['datasetKey']) || (isset($rArr['usage']['datasetKey']) && $rArr['usage']['datasetKey'] == $tArr['datasetKey'] )) break;
 						}
@@ -397,6 +413,9 @@ private function setColClassification(&$tArr, $subjectTaxonArr){
 			}
 			krsort($classificationArr);
 		}
+		if(isset($classificationArr[190]['sciname']) && !strpos($classificationArr[190]['sciname'], ' (')){
+			if(isset($classificationArr[180])) $classificationArr[190]['sciname'] = $classificationArr[180]['sciname'].' ('.$classificationArr[190]['sciname'].')';
+		}
 		if($classificationArr) $tArr['formattedClassification'] = $classificationArr;
 	}
 
@@ -515,7 +534,7 @@ private function addColChildern($id, $datasetKey, $nodeSciname, $parentTid, $ran
 							$this->logOrEcho($nodeArr['labelHtml'].' ('.$nodeArr['status'].') skipped due to extinct status',2);
 							continue;
 						}
-						$taxonArr = $this->translateColApiNode($nodeArr);
+						$taxonArr = $this->translateColNode($nodeArr);
 						$tid = $this->getTid($taxonArr);
 						if($tid){
 							$display = '<a href="'.$GLOBALS['CLIENT_ROOT'].'/taxa/taxonomy/taxoneditor.php?tid='.$tid.'" target="_blank">'.$nodeArr['labelHtml'].'</a>';
@@ -1150,9 +1169,9 @@ private function loadNewTaxon($taxonArr, $tidAccepted = 0){
 		}
 		if($loadTaxon){
 			if(!$newTid){
-			    if(isset($taxonArr['source']) && strlen($taxonArr['source']) > $this->taxaFieldArr['source']['size']){
-			        $taxonArr['source'] = substr($taxonArr['source'],0,$this->taxaFieldArr['source']['size']);
-			    }
+				if(isset($taxonArr['source']) && strlen($taxonArr['source']) > $this->taxaFieldArr['source']['size']){
+					$taxonArr['source'] = substr($taxonArr['source'],0,$this->taxaFieldArr['source']['size']);
+				}
 				$sqlInsert = 'INSERT INTO taxa(sciname, unitind1, unitname1, unitind2, unitname2, unitind3, unitname3, author, rankid, source, modifiedUid) '.
 					'VALUES("'.$this->cleanInStr($taxonArr['sciname']).'",'.
 					(isset($taxonArr['unitind1']) && $taxonArr['unitind1']?'"'.$this->cleanInStr($taxonArr['unitind1']).'"':'NULL').',"'.
@@ -1232,6 +1251,15 @@ private function loadNewTaxon($taxonArr, $tidAccepted = 0){
 					}
 					$this->logOrEcho('Taxon <b>'.$taxonDisplay.'</b> added to thesaurus as '.$accStr,2);
 				}
+				//Load taxonomic resources identifiers
+				if(isset($taxonArr['resourceURL'])){
+					$this->insertTaxonomicResource($newTid, 'Catalog of Life', $taxonArr['id'], $taxonArr['resourceURL']);
+				}
+				if(isset($taxonArr['sourceURL'])){
+					if(preg_match('/molluscabase.+\D+(\d+)$/', $taxonArr['sourceURL'], $m)){
+						$this->insertTaxonomicResource($newTid, 'MolluscaBase', $m[1], $taxonArr['sourceURL']);
+					}
+				}
 			}
 		}
 		//Add Synonyms
@@ -1361,6 +1389,15 @@ private function getParentArr($taxonArr){
 		return $parArr;
 	}
 
+	private function insertTaxonomicResource($tid, $sourceName, $sourceIdentifier, $sourceUrl){
+		$sql = 'INSERT INTO taxaresourcelinks(tid, sourceName, sourceIdentifier, url) VALUES(?, ?, ?, ?)';
+		if($stmt = $this->conn->prepare($sql)){
+			$stmt->bind_param('isss', $tid, $sourceName, $sourceIdentifier, $sourceUrl);
+			$stmt->execute();
+			$stmt->close();
+		}
+	}
+
 	//Misc functions
 	public function buildTaxonArr(&$taxonArr){
 		if(is_array($taxonArr)){
diff --git a/classes/TaxonomyUpload.php b/classes/TaxonomyUpload.php
index bd20749c46..408831a8d5 100644
--- a/classes/TaxonomyUpload.php
+++ b/classes/TaxonomyUpload.php
@@ -2,6 +2,7 @@
 include_once($SERVER_ROOT.'/config/dbconnection.php');
 include_once($SERVER_ROOT.'/classes/TaxonomyUtilities.php');
 include_once($SERVER_ROOT.'/classes/TaxonomyHarvester.php');
+include_once($SERVER_ROOT.'/classes/OccurrenceMaintenance.php');
 
 class TaxonomyUpload{
 
@@ -810,21 +811,10 @@ public function transferUpload(){
 		TaxonomyUtilities::buildHierarchyEnumTree($this->conn, $this->taxAuthId);
 
 		//Update occurrences with new tids
-		TaxonomyUtilities::linkOccurrenceTaxa($this->conn);
-
-		//Update occurrence images with new tids
-		$sql2 = 'UPDATE images i INNER JOIN omoccurrences o ON i.occid = o.occid '.
-			'SET i.tid = o.TidInterpreted '.
-			'WHERE (i.tid IS NULL) AND (o.TidInterpreted IS NOT NULL)';
-		$this->conn->query($sql2);
-
-		//Update geo lookup table
-		$sql3 = 'INSERT IGNORE INTO omoccurgeoindex(tid,decimallatitude,decimallongitude) '.
-			'SELECT DISTINCT o.tidinterpreted, round(o.decimallatitude,2), round(o.decimallongitude,2) '.
-			'FROM omoccurrences o '.
-			'WHERE (o.tidinterpreted IS NOT NULL) AND (o.decimallatitude between -90 and 90) AND (o.decimallongitude between -180 and 180) '.
-			'AND (o.cultivationStatus IS NULL OR o.cultivationStatus = 0) AND (o.coordinateUncertaintyInMeters IS NULL OR o.coordinateUncertaintyInMeters < 10000) ';
-		$this->conn->query($sql3);
+		$occurMaintenance = new OccurrenceMaintenance($this->conn);
+		$occurMaintenance->setCollidStr($this->collid);
+		$occurMaintenance->generalOccurrenceCleaning();
+		$occurMaintenance->batchUpdateGeoreferenceIndex();
 	}
 
 	private function transferVernaculars($secondRound = 0){
diff --git a/classes/TaxonomyUtilities.php b/classes/TaxonomyUtilities.php
index 16e9664a73..10f979ee57 100644
--- a/classes/TaxonomyUtilities.php
+++ b/classes/TaxonomyUtilities.php
@@ -339,28 +339,5 @@ private static function loadTaxonIntoNestedTree($conn, $tid, $taxAuthId, $startI
 		return $endIndex;
 	}
 	*/
-
-	public static function linkOccurrenceTaxa($conn = null){
-		if(!$conn) $conn = MySQLiConnectionFactory::getCon('write');
-
-		$sql1 = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname AND o.scientificnameauthorship = t.author SET o.TidInterpreted = t.tid WHERE (o.TidInterpreted IS NULL)';
-		if(!$conn->query($sql1)){
-			echo '<div>ERROR indexing occurrences by matching sciname and author</div>';
-		}
-
-		$sql2 = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname '.
-			'INNER JOIN taxaenumtree e ON t.tid = e.tid '.
-			'INNER JOIN taxa t2 ON e.parenttid = t2.tid '.
-			'SET o.TidInterpreted = t.tid '.
-			'WHERE (o.TidInterpreted IS NULL) AND (t2.rankid = 140) AND (t.sciname = o.family)';
-		if(!$conn->query($sql2)){
-			echo '<div>ERROR indexing occurrences by matching sciname and family</div>';
-		}
-
-		$sql3 = 'UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname SET o.TidInterpreted = t.tid WHERE (o.TidInterpreted IS NULL)';
-		if(!$conn->query($sql3)){
-			echo '<div>ERROR indexing occurrences by matching just sciname</div>';
-		}
-	}
 }
 ?>
\ No newline at end of file
diff --git a/collections/download/index.php b/collections/download/index.php
index 6863cb1831..8b98704769 100644
--- a/collections/download/index.php
+++ b/collections/download/index.php
@@ -195,6 +195,9 @@ function closePage(timeToClose){
 						<button type="submit" name="submitaction">Download Data</button>
 						<img id="workingcircle" src="../../images/ajax-loader_sm.gif" style="margin-bottom:-4px;width:20px;display:none;" />
 					</div>
+					<div class="sectionDiv">
+						* There is a 1,000,000 record limit to occurrence downloads
+					</div>
 				</fieldset>
 			</form>
 		</div>
diff --git a/collections/specprocessor/rpc/coge_build_dwca.php b/collections/specprocessor/rpc/coge_build_dwca.php
index b2f1d23ecd..92a903f0ac 100644
--- a/collections/specprocessor/rpc/coge_build_dwca.php
+++ b/collections/specprocessor/rpc/coge_build_dwca.php
@@ -46,7 +46,7 @@
 		if(substr($tPath,-1) != '/' && substr($tPath,-1) != '\\'){
 			$tPath .= '/';
 		}
-		$pathFrag = 'temp/data/geolocate/';
+		$pathFrag = 'temp/data/';
 		$tPath .= $pathFrag;
 		$dwcaHandler->setTargetPath($tPath);
 		$cnt = $dwcaHandler->getOccurrenceCnt();
diff --git a/config/symbbase.php b/config/symbbase.php
index f1e1b3fdc5..1e2079a44a 100644
--- a/config/symbbase.php
+++ b/config/symbbase.php
@@ -2,7 +2,7 @@
 header('X-Frame-Options: DENY');
 header('Cache-control: private'); // IE 6 FIX
 date_default_timezone_set('America/Phoenix');
-$CODE_VERSION = '3.0.5';
+$CODE_VERSION = '3.0.7';
 
 if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
 if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);
diff --git a/taxa/resourcetab.php b/taxa/resourcetab.php
index af81f764a6..3c600be3fe 100644
--- a/taxa/resourcetab.php
+++ b/taxa/resourcetab.php
@@ -24,6 +24,7 @@
 ?>
 <div id="tab-resource" class="sptab">
 	<?php
+	echo '<div class="resource-div">';
 	echo '<div class="resource-title">'.(isset($LANG['INTERNAL_RESOURCES'])?$LANG['INTERNAL_RESOURCES']:'Internal Resources').'</div>';
 	echo '<ul>';
 	$occNum = $taxonManager->getOccTaxonInDbCnt();
@@ -37,9 +38,11 @@
 	}
 	echo '<li><a href="taxonomy/taxonomydynamicdisplay.php?target='.$tid.'" target="_blank">Taxonomic Tree</a></li>';
 	echo '</ul>';
+	echo '</div>';
 	//TODO: list other internal resources such as Taxon Traits, etc
 
 	if($linkArr = $taxonManager->getLinkArr()){
+		echo '<div class="resource-div">';
 		echo '<div class="resource-title">'.(isset($LANG['EXTERNAL_RESOURCES'])?$LANG['EXTERNAL_RESOURCES']:'External Resources').'</div>';
 		echo '<ul>';
 		foreach($linkArr as $linkObj){
@@ -47,6 +50,18 @@
 			if($linkObj['notes']) echo '<li style="margin-left:10px">'.$linkObj['notes'].'</li>';
 		}
 		echo '</ul>';
+		echo '</div>';
+	}
+	if($resourceArr = $taxonManager->getResourceLinkArr()){
+		echo '<div class="resource-div">';
+		echo '<div class="resource-title">'.(isset($LANG['TAXONOMIC_RESOURCES'])?$LANG['TAXONOMIC_RESOURCES']:'Taxonomic Resources').'</div>';
+		echo '<ul>';
+		foreach($resourceArr as $resourceObj){
+			echo '<li><a href="'.$resourceObj['url'].'" target="_blank">'.$resourceObj['name'].' #'.$resourceObj['id'].($resourceObj['guid']?$resourceObj['guid']:'').'</a></li>';
+			if($resourceObj['notes']) echo '<li style="margin-left:10px">'.$resourceObj['notes'].'</li>';
+		}
+		echo '</ul>';
+		echo '</div>';
 	}
 	?>
 </div>
\ No newline at end of file