Bridging Genomics and Medicine by Ontology Fingerprints

描述（由申请人提供）： 由于两个领域之间的巨大差距，将基因组研究转化为临床实践面临着巨大的挑战。为了填补这一空白，我们提出了本体指纹的概念--一组在PubMed摘要中过度代表的本体术语，与基因或疾病沿着术语的相应富集p值，以表征基因和疾病。我们进一步通过比较基因和疾病之间的本体指纹来量化基因和疾病之间的关系-基因和疾病之间的本体指纹越相似，基因在疾病中发挥作用的可能性就越大。 假设：我们的首要假设是，通过开发生物医学本体和PubMed的本体指纹来弥合临床医学和基因组学之间的差距，可以实现对复杂疾病分子机制的新见解，并将这些见解转化为临床实践。首先将通过分析胃旁路手术（GBS）逆转糖尿病、肝脂肪变性和肥胖来评估这一总体假设。 具体目标：（1）通过比较生物医学文献中的人类基因的本体指纹和现有的生物医学本体，来检验可以构建新的基因网络的假设。(2)检验新的基因网络和本体指纹可用于破译GBS后糖尿病和肝脂肪变性逆转的分子机制的假设。(3)采用本体指纹技术，弥补基因组信息与临床医学之间的差距。 重要性：这些研究将把基因组信息与临床概念联系起来，并通过采用本体指纹来破译GBS后肥胖、糖尿病和肝脂肪变性的相互作用和逆转，将生物医学文献和基因组信息转化为临床实践。通过本体指纹弥合基因组学和医学之间的差距，将增强对患者的临床护理。

DESCRIPTION (provided by applicant): Translating genomic research into clinical practice faces tremendous challenges due to significant gaps between the two domains. To fill this gap, we have developed the concept of an ontology fingerprint - a set of ontology terms overrepresented in the PubMed abstracts linked to a gene or a disease along with the terms' corresponding enrichment p-value, to characterize genes and diseases. We further have quantified the relationship between a gene and a disease by comparing the ontology fingerprints of each - the more similar the ontology fingerprint between a gene and a disease, the more likely the gene plays a role in the disease. Hypothesis: Our overarching hypothesis is that new insights into the molecular mechanisms of complex diseases and translation of such insights into clinical practice can be achieved by developing ontology fingerprints from biomedical ontology and PubMed to bridge the gap between clinical medicine and genomics. This global hypothesis will be first evaluated by analyzing the reversal of diabetes, hepatic steatosis and obesity by gastric bypass surgery (GBS). Specific Aims: (1) test the hypothesis that a novel gene network can be constructed by comparing the ontology fingerprints of human genes derived from the biomedical literature and available biomedical ontologies. (2) test the hypothesis that the novel gene network and ontology fingerprints can be used to decipher the molecular mechanisms of the reversal of diabetes and hepatic steatosis following GBS. (3) deploy ontology fingerprint to bridge the gap between genome information and clinical medicine. Significance: These studies will link genomic information to clinical concepts and translate biomedical literature and genomic information into clinical practice by employing ontology fingerprints to decipher the interplay and reversal of obesity, diabetes and hepatic steatosis after GBS. Bridging the gap between genomics and medicine by ontology fingerprints will enhance the delivery of clinical care to patients.