NCBI xml-format Printing nodeValues from tags with the same names

Question

I would like to retrieve all Other-source_anchor on the level of DNA binding from within a Gene Ontology XML file using php.

If I try this with my code, I only get Gene Ontology back and not the nodeValues in Other-source_anchor. Could someone tell me how to do this?

Xml file were I wwant to get the nodeValues from

<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>

code:

$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->nodeName."</pre>";
        echo "<pre>"."$c: ".$node->nodeValue."</pre>";
        $cn = 1;
        foreach ($node->getElementsByTagName('Other-source_anchor') as $subnode){
            echo "<pre>"."$c: ".$subnode->nodeName."</pre>";
            echo "<pre>"."$c: ".$subnode->nodeValue."</pre>"; 

            echo $cn++;
        }
    }
    $c++;
} 

Answer 1

use a XSLT processor (http://php.net/manual/en/class.xsltprocessor.php) with the following stylesheet.

<?xml version='1.0' encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' version='1.0'>
    <xsl:output method="html"/>

    <xsl:template match="/">
        <div>
            <xsl:apply-templates select="//Gene-commentary_heading[ text() = 'GeneOntology']"/>
        </div>
    </xsl:template>

    <xsl:template match="Gene-commentary_heading">
        <pre><xsl:value-of select="name(.)"/></pre>
        <pre><xsl:value-of select="."/></pre>
        <xsl:apply-templates select="..//Other-source_anchor"/>
    </xsl:template>

    <xsl:template match="Other-source_anchor">
        <pre><xsl:value-of select="name(.)"/></pre>
        <pre><xsl:value-of select="."/></pre>
    </xsl:template>

</xsl:stylesheet>