Merge branch 'release3' of github.com:micheldumontier/bio2rdf-scripts into release3

Author: micheldumontier

ncbigene/ncbigene.php

@@ -66,7 +66,7 @@ function __construct($argv) {
 		// set and print application parameters
 		parent::addParameter('files',true,'all|geneinfo|gene2accession|gene2ensembl|gene2go|gene2pubmed|gene2refseq|gene2sts|gene2unigene|gene2vega','','files to process');
 		parent::addParameter('download_url',false,null,'ftp://ftp.ncbi.nih.gov/gene/DATA/');
-		parent::addParameter('limit_organisms',false,'true|false','false','flag to use specified organisms');
+		parent::addParameter('limit_organisms',false,'true|false','true','flag to use specified organisms');
 		parent::addParameter('organisms',false,null,implode(",",array_keys($this->default_taxids)),'taxonomy ids for organisms to process');
 		parent::initialize();
 	}//constructor

taxonomy/taxonomy.php

@@ -157,7 +157,7 @@ public function Run(){
 						|| $k == "gencode" || $k == "division" 
 						|| $k == "gi_taxid_prot" || $k == "gi_taxid_nucl"){
 
-if($k !== 'names') continue;
+//if($k !== 'citations') continue;
 						$fpin = $zin->getStream($fn);
 
 						if(!$fpin){