Big Data approaches to host-pathogen mapping: EID2 - an open-access, taxonomically- and spatially-referenced database of pathogens and their hosts

人类以及与我们密切相关的动物的已知病原体是什么，并因此可能传播给我们？我们吃的植物的已知病原体都是什么？这些病原体到底在哪里找到的呢？普通公众可能会惊讶于这些问题的答案很难获得。最近(2013年)的一项估计是，只有大约五分之一的人类疾病被全面绘制出来，动植物疾病的情况可能更糟。近年来，利物浦大学创建了一个开放获取的人类和动物病原体数据库，称为增强型传染病数据库或EID2。它存储关于病原体、它们的宿主以及在世界上哪里发现两者的信息，在国家和次国家(即州或地区)一级。所有数据都与证据有关。输入数据库的数据主要来自三个公开可用的在线资源：分类数据库(描述病原体或宿主是哪种生物--病毒、昆虫、哺乳动物等)；核苷酸序列数据库(提供关于病原体的宿主和位置的信息)；以及出版物数据库PubMed。重要的是，数据是通过自动化程序从这些数据源获得的，因此可以相对较少的工作定期更新数据。这一点很重要，因为，例如，我们的信息来源之一Genbank中输入的核苷酸序列的数量每年接近1000万；每年有100多万篇新论文被PubMed(NCBI统计数据)索引。我们预计EID2将成为参与健康相关研究的人和其他健康专业人员的主要资源。EID2中的数据量已经很大，随着时间的推移，随着更多的数据变得可用并自动输入到数据库中，我们希望它将变得更加全面，并成为病原体/疾病信息的最终来源。EID2提供了许多功能：识别宿主的病原体、病原体的宿主、特定国家或地区的已知病原体、病原体的分布图等。这项建议的目的是扩展数据库以包括农作物的病原体，增加关于应报告的动物疾病的新数据流，使其更全面和及时，当新数据可用时定期更新它，提高其功能和速度，允许用户请求更改和下载定制的数据输出，不断评估其准确性，并将其推广到研究和其他社区。

What are all of the known pathogens of humans, and those of the animals that associate closely with us, and hence might spread to us? What are all of the known pathogens of the plants that we eat? And where in the world are these pathogens found? The general public may be surprised that answers to these questions are hard to obtain. A recent (2013) estimate is that only about one in fifty of human diseases have been comprehensively mapped, and the situation for animal and plant diseases is probably worse.In recent years the University of Liverpool has created an open-access database of human and animal pathogens, called the ENHanCED Infectious Diseases database or EID2. It stores information on pathogens, their hosts, and where both are found in the world, at national and sub-national (i.e. state or region) levels. All data are linked to evidence. The data entered into the database is obtained largely from three publicly available online resources: a taxonomy database (which describes which sort of organism a pathogen or host is - virus, insect, mammal etc.); a nucleotide sequence database (which provides information on the hosts and locations of pathogens); and a publication database called PubMed. Importantly, the data is obtained from these data sources by automated procedures, such that they can be regularly updated for relatively little effort. This is important as, for example, the numbers of nucleotide sequences entered into Genbank, one source of our information, is approaching 10 million per year; and there are over 1 million new papers indexed annually by PubMed (NCBI statistics).We expect EID2 to become a major resource for people involved in health-related research, and other health professionals. The volume of data in EID2 is already large and, over time, as more data become available and are automatically entered into the database, we hope it will become more comprehensive, and the definitive source of pathogen/disease information.EID2 offers numerous functions: identifying the pathogens of hosts, the hosts of pathogens, the known pathogens of a specific country or region, maps of the distribution of pathogens, and more besides.The aim of this proposal is to expand the database to include the pathogens of crop plants, add a new data stream for notifiable animal diseases which will make it more comprehensive and timely, update it regularly as new data become available, increase its functionality and speed, allow users to request changes and download bespoke data outputs, continually assess its accuracy, and promote its use to research and other communities.