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

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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.