Удалите все теги html из строки, оставив только один из них. Расширенные strip_tags с одним атрибутом идентификатора

Для этого вам понадобится несколько regex.

Рабочий код:

<?php
    header("Content-Type: text/plain");

    $str = '<!-- comment -->   <div id="55"> text </div> <span name=annotation value=125> 2 text </span> <p id="55"> text 3</p><span>text 4 </span>';

    // Save needed values
    $str = preg_replace("/<(span[^>]*?annotation.*?)>(.*?)<\/(.*?)>/", "!!!$1!!!$2!!!$3!!!", $str); 

    // Remove everything else
    $re = "/(<[^>]*?>)/";
    $str = preg_replace($re, "", $str);

    // Restore
    $str = preg_replace("/\!\!\!(span[^>]*?annotation.*?)\!\!\!(.*?)\!\!\!(.*?)\!\!\!/", "<$1>$2</$3>", $str); 

    echo $str;
?>

Выход:

text  <span name=annotation value=125> 2 text </span>  text 3text 4 

Вход:

$str='<!-- comment --><p><b>Deoxyribonucleic acid</b> (<b>DNA</b>) is 
   a molecule encoding the <a href="/wiki/Genetics" title="Genetics">genetic</a> instructions
   used in the development and functioning of all known living <a href="/wiki/Organism" title="Organism">organi
   sms</a> and many <a href="/wiki/Virus" title="Virus">viruses</a>. Along with <a href="/wiki/RNA" title="RNA">RNA</a> and <a href="/wiki/Proteins" title="Proteins" class="mw-redirect">proteins</a>, DNA is one of the three major 
   <a href="/wiki/Macromolecules" title="Macromolecules" class="mw-redirect">macromolecules</a> 
   that are essential for all known forms of <a href="/wiki/Life" title="Life">life</a>.
   Genetic information is encoded<span id="200120131815150" 
   class="mymetastasis" value="247" name="annotation"> as a sequence of nucleotides (</span><a href="/wiki/Guanine" title="Guanine"><span id="200120131815151" class="mymetastasis" value="247" name="annotation">
   guanine</span></a><span id="200120131815152" class="mymetastasis" value="247" name="annotation">, </span><a href="/wiki/Adenine" title="Adenine"><span id="200120131815153" class="mymetastasis" value="247"
   name="annotation">adenine</span></a><span id="200120131815154" class="mymetastasis" value="247" name="annotation">,
   </span><a href="/wiki/Thymine" title="Thymine"><span id="200120131815155" class="mymetastasis" value="247"
   name="annotation">thymine</span></a><span id="200120131815156" class="mymetastasis" value="247" name="annotation">, 
   and </span><a href="/wiki/Cytosine" title="Cytosine">
   <span id="200120131815157" class="mymetastasis" value="247" name="annotation">cytosine</span></a><span id="200120131815158" class="mymetastasis" value="247" name="annotation">) 
   recorded using the letters G, A, T, and C. Most DNA molecules are double-strande</span>d helices, consisting of two long <a href="/wiki/Polymers" title="Polymers" class="mw-redirect">polymers</a> of simple units called <a href="/wiki/Nucleotide" 
   title="Nucleotide">nucleotides</a>, molecules with <a href="/wiki/Backbone_chain" title="Backbone chain">backbones</a>
   made of alternating <a href="/wiki/Monosaccharide" title="Monosaccharide">sugars<
   /a> (<a href="/wiki/Deoxyribose" title="Deoxyribose">deoxyribose</a>) and <a href="/wiki/Phosphate"
   title="Phosphate">phosphate</a> groups (related to phosphoric acid), with the <a href="/wiki/Nucleobases" title="Nucleobases" class="mw-redirect">nucleobases</a> (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a 
   built-in duplicate of the encoded information.</p>';

Выход:

Deoxyribonucleic acid (DNA) is 
   a molecule encoding the genetic instructions
   used in the development and functioning of all known living organi
   sms and many viruses. Along with RNA and proteins, DNA is one of the three major 
   macromolecules 
   that are essential for all known forms of life.
   Genetic information is encoded<span id="200120131815150" 
   class="mymetastasis" value="247" name="annotation"> as a sequence of nucleotides (</span>
   guanine<span id="200120131815152" class="mymetastasis" value="247" name="annotation">, </span><span id="200120131815153" class="mymetastasis" value="247"
   name="annotation">adenine</span>,
   <span id="200120131815155" class="mymetastasis" value="247"
   name="annotation">thymine</span>, 
   and 
   <span id="200120131815157" class="mymetastasis" value="247" name="annotation">cytosine</span>) 
   recorded using the letters G, A, T, and C. Most DNA molecules are double-stranded helices, consisting of two long polymers of simple units called nucleotides, molecules with backbones
   made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a 
   built-in duplicate of the encoded information.

В PHP для этого есть встроенная функция, которая называется strip_tags.

Если вы хотите сохранить только тег span, используйте второй аргумент.

So,

$cleanString = strip_tags($dirtyString, '<span>');