Ammari Mais G, Gresham Cathy R, McCarthy Fiona M, Nanduri Bindu
School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA.
Institute for Genomics, Biocomputing and Biotechnology, College of Veterinary Medicine, Institute for Genomics, Mississippi State University, Mississippi State, MS 39762, USA.
Database (Oxford). 2016 Jul 3;2016. doi: 10.1093/database/baw103. Print 2016.
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.Database URL: http://www.agbase.msstate.edu/hpi/main.html.
宿主-病原体相互作用（HPI）的识别与分析对于研究传染病至关重要。然而，现有分子相互作用数据库中的HPI数据较为稀少，特别是针对农业宿主-病原体系统。因此，注释、预测和展示构成传染病基础的HPI的资源对于开发新型干预策略至关重要。HPIDB 2.0（http://www.agbase.msstate.edu/hpi/main.html）是一个HPI数据资源库，当前版本包含45,238条人工整理的条目。自2010年首次描述该数据库以来，对HPIDB的数据和接口服务进行了多次改进，在此进行介绍。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注释。作为国际分子交换联盟的成员，HPIDB 2.0的注释者提供的注释符合社区标准，以提供详细的背景实验信息并促进数据共享。此外，HPIDB 2.0提供对快速可用的社区注释的访问，这些注释捕获了最小的分子相互作用信息，以满足研究人员对HPI网络分析的即时需求。除了注释外，HPIDB 2.0整合了来自现有外部来源的HPI，并包含在注释数据稀缺时推断其他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的用户能够从广泛的病原体及其宿主（截至2016年2月为594种病原体和70种宿主物种）中获取最全面的HPI数据。改进还包括增强搜索能力、添加基因本体功能信息以及实现网络可视化。对HPIDB 2.0内容和接口所做的更改确保用户，尤其是农业研究人员，能够轻松访问和分析高质量、全面的HPI数据。HPIDB 2.0的所有数据均定期更新，可公开直接下载，并分发至其他分子相互作用资源。数据库网址：http://www.agbase.msstate.edu/hpi/main.html 。
