HPIDB 2.0: a curated database for host-pathogen interactions
HPIDB 2.0: a curated database for host-pathogen interactions
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DOI：
10.1093/database/baw103
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发表时间：
2016-07-03
影响因子：
5.8
通讯作者：
Nanduri, Bindu
中科院分区：
文献类型：
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作者：
Ammari, Mais G.;Gresham, Cathy R.;Nanduri, Bindu
宿主-病原体相互作用（HPI）的识别和分析是研究传染病的关键。然而，HPI数据稀疏在现有的分子相互作用数据库，特别是农业寄主-病原体系统。因此，注释、预测和显示支撑传染病的HPI的资源对于开发新的干预策略至关重要。HPIDB 2.0（http：//www.agbase.msstate.edu/hpi/main.html）是HPI数据的资源，在当前版本中包含45，238个手动管理的条目。自2010年首次描述该数据库以来，对HPIDB数据和接口服务进行了多次增强，如本文所述。值得注意的是，HPIDB 2.0现在提供分子相互作用数据的靶向生物定位。作为国际分子交换联盟的成员，HPIDB 2.0策展人提供的注释符合社区标准，以提供详细的上下文实验信息并促进数据共享。此外，HPIDB 2.0提供了快速获得社区注释，捕获最小的分子相互作用信息，以满足HPI网络分析的即时研究需求。除了策展之外，HPIDB 2.0还集成了来自现有外部资源的HPI，并包含用于在注释数据稀缺的情况下推断其他HPI的工具。与其他相互作用数据库相比，我们的数据收集方法确保HPIDB 2.0用户访问来自广泛病原体及其宿主（截至2016年2月，594种病原体和70种宿主物种）的最全面的HPI数据。改进还包括增强的搜索能力，基因本体功能信息的添加，以及网络可视化的实现。对HPIDB 2.0内容和界面所做的更改确保用户，特别是农业研究人员，能够轻松访问和分析高质量、全面的HPI数据。所有HPIDB 2.0数据定期更新，可直接下载，并传播到其他分子相互作用资源。
Identification and analysis of host-pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host-pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources.