Rare Disease analysis in Mondo

To answer the question of 'How many rare diseases are there?' we analyzed terms in Mondo to get a total count of Rare Diseases as defined in Mondo Disease Ontology (Mondo). Methods This analysis was performed on the Mondo 2019-09-30 release. <strong>1. Get all 'Disease' terms from Mondo</strong> First we get all the terms in Mondo that are a descendants of <code>MONDO:0000001 'Disease'</code>. There are <code>21633</code> Mondo disease terms. <strong>2. Filter terms that are descendants of 'disease susceptibility'</strong> We then filter out terms that are descendants of <code>MONDO:0042489 'disease susceptibility'</code>, to avoid counting ambiguous terms that are related to disease susceptibility and not the actual disease itself. This gives us a list of <code>21563</code> Mondo rare disease terms. <strong>3. Identify terms that are 'rare'</strong> Any disease term in Mondo is considered rare if the term, or its ancestor, has modifier <code>MONDO:0021136 'Rare'</code> in the ontology. There are <code>12914</code> Mondo rare disease terms. <strong>4. Consider terms in 'gard_rare' subset</strong> 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 'rare'. We add these terms to our set of Mondo rare disease terms. This increases the Mondo rare disease term count to <code>13866</code>. But for this analysis, we are interested in terms that are both rare and are leaf nodes in the ontology. After considering only leaf nodes, we get <code>10394</code> as the final count of Mondo rare disease terms. Results 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.为解答“罕见病共有多少种？”这一问题，本研究针对Mondo疾病本体（Mondo Disease Ontology）中的术语开展分析，以统计该本体定义下的罕见病总数量。 **分析方法**：本分析基于Mondo 2019-09-30版本数据集完成。 1. **提取Mondo中所有“疾病”类术语**：首先获取Mondo本体中所有为`MONDO:0000001 '疾病（Disease）'`的后代术语，共计21633个Mondo疾病术语。 2. **过滤“疾病易感性”类后代术语**：随后剔除属于`MONDO:0042489 '疾病易感性（disease susceptibility）'`后代的术语，以避免将与疾病易感性相关而非真正疾病本身的歧义术语纳入统计，最终得到21563个候选Mondo疾病术语。 3. **识别“罕见”类术语**：若Mondo中的某疾病术语自身或其祖先本体中带有修饰符`MONDO:0021136 '罕见（Rare）'`，则将其认定为罕见病术语，共计12914个Mondo罕见病术语。 4. **纳入`gard_rare`子集术语**：Mondo本体中另有3176个疾病术语属于`gard_rare`子集，该子集包含尚未被标记为“罕见”的Mondo术语。将此类术语加入前述罕见病术语集合后，Mondo罕见病术语总数增至13866个。但本分析仅关注同时满足“罕见”且为本体叶节点的术语，经筛选后最终得到Mondo罕见病术语的统计结果为10394个。 **分析产物**：本分析生成了TSV格式文件`all-mondo-disease-terms.tsv`，其中包含21633个Mondo疾病术语，每个术语均附带注释信息，用于标记该术语是否为罕见病术语，以及是否为本体中的叶节点。