Via the link [https://www.ncbi.nlm.nih.gov/gene/7128?report=xml&format=text][1] I retrieved an XML format. From this format I retrieved all information between Gene-commentary_headings. Therefore I used DOMDocuments and getElemenetsByTagName. Now, I am trying to retrieve the line; for example with name GeneOntology. GeneOntology is located by the 22 tag of Gene-commmentary_heading. I retrieve only the information that is located within the part of the Gene-commentary_headings.
<Gene-commentary_heading>GeneOntology</Gene-commentary_heading>.
Now, I am trying to print for example all tags with the name Other-source_anchor. For example
<Other-source_anchor>DNA binding</Other-source_anchor>
But there is also on GOA with the same tag but at higher level. I would like only to retrieve the tags at the level of DNA binding. If I use
foreach($node->getElementsByTagName('Other-source_anchor') as $subnode)
I get no result. if I change $node by $doc, I retrieve all the nodeValues with the tag. How do I make sure that I only retrieve the nodeValues of the Other-source_anchor tag at the level of DNA binding?
Bellow is the code I wrote:
$esearch_test = "https://www.ncbi.nlm.nih.gov/gene/7128?report=xml&format=text";
$result = file_get_contents($esearch_test);
$xml = simplexml_load_string($result);
$doc = new DOMDocument();
$doc = DOMDocument::loadXML($xml);
$c = 1;
foreach($doc->getElementsByTagName('Gene-commentary_heading') as $node) {
if ($node->textContent =="GeneOntology"){
// echo "<pre>"."$c: ".$node->textContent."</pre>";
// echo "<pre>"."$c: ".$node->nodeName."</pre>";
// echo "<pre>"."$c: ".$node->nodeValue."</pre>";
foreach ($doc->getElementsByTagName('Other-source_anchor') as $subnode){
echo "<pre>"."$c: ".$subnode->nodeName."</pre>";
echo "<pre>"."$c: ".$subnode->nodeValue."</pre>";
}
}
$c++; # 22: GeneOntology
}
Part of the xml file I am using in the code above.
<Gene-commentary_heading>**GeneOntology**</Gene-commentary_heading>
<Gene-commentary_source>
<Other-source>
<Other-source_pre-text>Provided by</Other-source_pre-text>
<Other-source_anchor>GOA</Other-source_anchor>
<Other-source_url>http://www.ebi.ac.uk/GOA/</Other-source_url>
</Other-source>
</Gene-commentary_source>
<Gene-commentary_comment>
<Gene-commentary>
<Gene-commentary_type value="comment">254</Gene-commentary_type>
<Gene-commentary_label>Function</Gene-commentary_label>
<Gene-commentary_comment>
<Gene-commentary>
<Gene-commentary_type value="comment">254</Gene-commentary_type>
<Gene-commentary_source>
<Other-source>
<Other-source_src>
<Dbtag>
<Dbtag_db>GO</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>3677</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
</Other-source_src>
<Other-source_anchor>DNA binding</Other-source_anchor>
<Other-source_post-text>evidence: IEA</Other-source_post-text>
</Other-source>
</Gene-commentary_source>
</Gene-commentary>
<Gene-commentary>
Function that retrieve the information for a given path in string format
function xml_retriever($xml_link,$path){
$result = file_get_contents($xml_link);
$xml = simplexml_load_string($result);
$doc = new DOMDocument();
$doc = DOMDocument::loadXML($xml);
$xpath = new DOMXPath($doc);
$entries = $xpath->query($path);
$attr = '';
foreach($entries as $node){
$attr .= '|'.' '.$node->nodeValue. "\r\n";
$attr = ltrim($attr, '|');
}
return $attr;
}
Simple test if the function works
# Example query and example path
$esearch_test = "https://www.ncbi.nlm.nih.gov/gene/7128?report=xml&format=text";
$query = "/Entrezgene/Entrezgene_properties/Gene-commentary[3]/Gene-commentary_comment/Gene-commentary[1]/Gene-commentary_comment/Gene-commentary[*]/Gene-commentary_source/Other-source/Other-source_anchor";
# Print the result
echo xml_retriever($esearch_test,$query);