联合的SPARQL查询性能评估用于探索疾病模型小鼠:结合基因表达,正义学和疾病知识图表
Tatsuya Kushida1, Tarcisio Mendes de Farias2,3, Ana C Sima2
1BioResource Research Center, RIKEN, Tsukuba-shi, Japan. tatsuya.kushida@riken.jp.
BMC medical informatics and decision making
|May 16, 2025
概括
这项研究整合了多个生物资源数据库,以确定与疾病相关的基因和模型生物用于研究. 通过改进数据传输和增强服务器规格,优化了查询性能.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 生物医学研究生物医学研究
背景情况:
- 瑞肯生物资源元数据库有助于生物资源的探索.
- 瑞士生物信息学研究所维护Bgee和OMA基因表达和骨科的数据库.
研究的目的:
- 评估在医学研究中选择模型生物的分布式SPARQL查询性能.
- 将RIKEN BioResource数据与多个RDF数据集 (Bgee,OMA,DisGeNET,MGI,UniProt,本体学) 集成在一起.
- 识别与疾病相关的基因,它们的表达模式,以及特定研究应用的相关生物资源.
主要方法:
- 结合了RIKEN生物资源数据与来自Bgee,OMA,DisGeNET,MGI,UniProt和疾病本体学的RDF数据集.
- 利用SPARQL查询来调查与疾病相关的基因及其解剖表达.
- 用户物业路径用于Uber的过渡性搜索.
- 将联合的SPARQL查询性能与集中查询进行比较.
主要成果:
- 确定了14个与阿尔茨海默病相关的基因 (例如,APP,APOE) 在前额叶皮质表达.
- 发现了55个与阿尔茨海默病研究相关的RIKEN生物资源 (转基因小鼠).
- 确定了14个与黑色素瘤相关的基因 (例如HRAS,PTEN) 和12个表达解剖部位 (例如肢体皮肤) 的基因.
结论:
- 联邦 SPARQL 查询性能降低.
- 通过通过子查询提炼传输的数据来优化联合查询性能.
- 增强了服务器规范,以改善三重存储查询评估并减少性能退化.
关键词:
数据库集成数据库集成基因表达 基因表达 基因表达基因与疾病的关联知识图表知识图表模型生物模型生物.存在论 (Ontology) 是一种存在论.正统学正统学是一门学科.在RDF中使用RDF.SPARQL SPARQL 在线播放更多相关视频
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