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added 'all' parameter to constructor, and separated with a dash the rdf:type being used
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hgnc/hgnc.php

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,8 @@ class HGNCParser extends Bio2RDFizer {
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private $version = 2.0;
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function __construct($argv){
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parent::__construct($argv, "hgnc");
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parent::addParameter('files', true, 'hgnc_complete_set', 'hgnc_complete_set', 'The filename of the complete HGNC dataset');
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//parent::addParameter('files', true, 'hgnc_complete_set', 'hgnc_complete_set', 'The filename of the complete HGNC dataset');
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parent::addParameter('files',true,'all','all','files to process');
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parent::addParameter('download_url',false,null,'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc_complete_set.txt.gz');
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parent::initialize();
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}//constructor
@@ -156,7 +157,7 @@ function process(){
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$id_label = "hgnc identifier";
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$id_label_class = "hgnc identifier: ".$id;
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parent::AddRDF(
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parent::triplify($id_res, "rdf:type", $this->getVoc()."GeneSymbol").
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parent::triplify($id_res, "rdf:type", $this->getVoc()."Gene-Symbol").
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parent::describeIndividual($id_res, $id_label, $this->getVoc()."gene symbol").
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parent::describeClass($this->getVoc()."GeneSymbol", $id_label_class)
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);

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