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Computational methods for the study of human disease manifestations: The Human Phenotype Ontology
... HPO is able to capture phenotypic similarities between diseases in a useful and highly significant fashion. With the spread of HPO, more and more calculation methods are gradually applied in the diagnosis of human genetic diseases and finally enable the exploration of characterization data [37]. For example, groups of Köhler adapted semantic similarity metrics to measure phenotypic similarity between queries and hereditary diseases annotated with the use of the HPO and have developed a statistical model to assign values to the resulting similarity scores, which can be used to rank the candidate diseases [38]. ...
The characteristics of holistic, dynamics, complexity, and spatial and temporal features enable "Omics" and theories of TCM to interlink with each other. HPO, namely, "characterization," can be understood as a sorting and generalization of the manifestations shown by people with diseases on the basis of the phenomics. Syndrome is the overall "manifestation" of human body pathological and physiological changes expressed by four diagnostic methods' information. The four diagnostic methods' data could be the most objective and direct manifestations of human body under morbid conditions. In this aspect, it is consistent with the connation of "characterization." Meanwhile, the four diagnostic methods' data also equip us with features of characterization in HPO. In our study, we compared 107 pieces of four diagnostic methods' information with the "characterization database" to further analyze data of four diagnostic methods' characterization in accordance with the common characteristics of four diagnostic methods' information and characterization and integrated 107 pieces of four diagnostic methods' data to relevant items in HPO and finished the expansion of characterization information in HPO.
... The analysis of molecular mechanism is undertaken by Pathway Pattern-based method [24] and MetaDrug platform [25], respectively, to correlate symptoms with Pathway Pattern, uncover enriched pathways and construct the most relevant interaction network. By referring to the Human Phenotype Ontology (HPO) [32][33][34], we bridged the gap between symptoms and genes. Firstly, we searched the ontology file for HPO terms which describe phenotypic abnormalities that have similar meaning with the core symptoms. ...
Prompt and accurate diagnosis of acute ischemic stroke is critical to seek acute therapy. In traditional Chinese medicine (TCM) science, there is a comprehensive system of diagnosis and medical care of acute ischemic stroke. Here we introduce a two-level model for the analysis of TCM syndrome of acute ischemic stroke. Owing to the limitation of sample size and imbalance, we focused on the analysis of wind-phlegm collateral obstruction syndrome (Feng Tan Yu Zu Zheng). Firstly, a Support-Vector-Machine- (SVM-) based diagnostic model was set up through selection of core symptoms. After pairwise undersampling, we improved the performance of prediction and generated the core symptoms-based diagnostic model of wind-phlegm collateral obstruction syndrome. Next, Pathway Pattern-based method and MetaDrug platform were used to shed light on the molecular basis of the significance of core symptoms in three complementary aspects: symptom-gene-pathway multilayer correlation network, enriched pathways, and most relevant interaction network. The integration of diagnostic model and molecular mechanism analysis creates an interesting perspective for better understanding the syndrome. The two-level model would provide a new opportunity for the study of TCM syndromes.
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