Similarity Calculation, Enrichment Analysis, and Ontology Visualization of Biomedical Ontologies using UFO

2021 ◽  
Vol 1 (4) ◽  
Author(s):  
Quang‐Huy Nguyen ◽  
Duc‐Hau Le
Keyword(s):  
Enrichment Analysis ◽  
Biomedical Ontologies ◽  
Similarity Calculation ◽  
Ontology Visualization

scholarly journals Best Paper Selection

2021 ◽  
Vol 30 (01) ◽  
pp. 189-189
Keyword(s):  
Semantic Similarity ◽  
Likelihood Ratio ◽  
Enrichment Analysis ◽  
Biomedical Ontology ◽  
Biomedical Ontologies ◽  
Clinical Genomics ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language ◽  
Similarity Calculation

Le DH. UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235670 Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL, Core UNCB, Karlebach G, Reese J, Holtgrewe M, Kohler S, McMurry JA, Haendel MA, Smedley D. Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. https://www.cell.com/ajhg/fulltext/S0002-9297(20)30230-5 Slater LT, Gkoutos GV, Hoehndorf R. Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-020-01336-2 Zheng F, Shi J, Yang Y, Zheng WJ, Cui L. A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. https://pubmed.ncbi.nlm.nih.gov/32918476/

A Method of Pathway Enrichment Analysis Based Gene Expression Variability

2013 ◽  
Vol 40 (12) ◽  
pp. 1256
Author(s):  
XiaoDong JIA ◽  
XiuJie CHEN ◽  
Xin WU ◽  
JianKai XU ◽  
FuJian TAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Expression Variability ◽  
Pathway Enrichment
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