Rare Disease analysis in Mondo

<p>To answer the question of &#39;How many rare diseases are there?&#39; we analyzed terms in Mondo to get a total count of Rare Diseases as defined in Mondo Disease Ontology (Mondo).</p> <p>&nbsp;</p> <p>Methods</p> <p>This analysis was performed on the <a href="http://purl.obolibrary.org/obo/mondo/releases/2019-09-30/mondo.json">Mondo 2019-09-30 release</a>.</p> <p><strong>1. Get all &#39;Disease&#39; terms from Mondo</strong></p> <p>First we get all the terms in Mondo that are a descendants of <code>MONDO:0000001 &#39;Disease&#39;</code>.</p> <p>There are <code>21633</code> Mondo disease terms.</p> <p><strong>2. Filter terms that are descendants of &#39;disease susceptibility&#39;</strong></p> <p>We then filter out terms that are descendants of <code>MONDO:0042489 &#39;disease susceptibility&#39;</code>, to avoid counting ambiguous terms that are related to disease susceptibility and not the actual disease itself.</p> <p>This gives us a list of <code>21563</code> Mondo rare disease terms.</p> <p><strong>3. Identify terms that are &#39;rare&#39;</strong></p> <p>Any disease term in Mondo is considered rare if the term, or its ancestor, has modifier <code>MONDO:0021136 &#39;Rare&#39;</code> in the ontology.</p> <p>There are <code>12914</code> Mondo rare disease terms.</p> <p><strong>4. Consider terms in &#39;gard_rare&#39; subset</strong></p> <p>There are <code>3176</code> Mondo disease terms that are in <code>gard_rare</code> subset which contains Mondo terms that are yet to be treated as &#39;rare&#39;.</p> <p>We add these terms to our set of Mondo rare disease terms.</p> <p>This increases the Mondo rare disease term count to <code>13866</code>.</p> <p>But for this analysis, we are interested in terms that are both rare and are leaf nodes in the ontology.</p> <p>After considering only leaf nodes, we get <code>10394</code> as the final count of Mondo rare disease terms.</p> <p>&nbsp;</p> <p>Results</p> <p>all-mondo-disease-terms.tsv: As part of our analysis, we generated a TSV containing 21633 Mondo disease terms, each with annotations that signifies whether the term is a rare disease term and whether that term is a leaf node in the ontology.</p>