转录调控数据的语义集成。
Semantic integration of data on transcriptional regulation.
机构信息
San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
出版信息
Bioinformatics. 2010 Jul 1;26(13):1651-61. doi: 10.1093/bioinformatics/btq231. Epub 2010 Apr 28.
MOTIVATION
Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources. However, there are no resources to integrate these data automatically or to provide a 'one-stop shop' experience for users seeking information essential for deciphering and modeling gene regulatory networks.
RESULTS
IntegromeDB, a semantic graph-based 'deep-web' data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information, is proposed in this article. The problems associated with data integration are addressed by ontology-driven data mapping, multiple data annotation and heterogeneous data querying, also enabling integration of the user's data. IntegromeDB integrates over 100 experimental and computational data sources relating to genomics, transcriptomics, genetics, and functional and interaction data concerning gene transcriptional regulation in eukaryotes and prokaryotes.
AVAILABILITY
IntegromeDB is accessible through the integrated research environment BiologicalNetworks at http://www.BiologicalNetworks.org
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
有关基因转录调控的实验和预测数据分布在许多异构源中。然而，目前还没有资源可以自动整合这些数据，也无法为用户提供一个“一站式”的体验，以获取破译和构建基因调控网络所需的关键信息。
结果
本文提出了 IntegromeDB，这是一个基于语义图的“深网”数据集成系统，可自动捕获、整合和管理有关转录调控以及其他相关生物学信息的公开可用数据。通过本体驱动的数据映射、多数据注释和异构数据查询解决了数据集成问题，还支持用户数据的集成。IntegromeDB 集成了超过 100 个与基因组学、转录组学、遗传学以及真核生物和原核生物基因转录调控的功能和相互作用数据相关的实验和计算数据源。
可用性
IntegromeDB 可通过集成研究环境 BiologicalNetworks 在 http://www.BiologicalNetworks.org 上访问。
联系信息
补充信息
补充数据可在 Bioinformatics 在线获得。
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