What, where and weather? Integrating open-source taxonomic, spatial and climatologic information into a comprehensive database of livestock infections

What are all the species of pathogen that affect our livestock? It is important to answer this question, to help protect the animals that produce our food, and also because nearly 7 out of every 10 human pathogens came from animals, with a good number from the livestock and pets that we closely associate with. Remarkably, however, even for humans this question was only answered ten years ago (1415 were listed) and there remains no definitive answer for livestock, domestic pets and other animals.
This proposal aims to further develop a new database of livestock (and other) pathogens, called EID2 (ENHanCED Infectious Diseases 2). EID2 has been built largely from the tens of millions of records of DNA and RNA sequences that are uploaded onto public databases; where such sequences are from a pathogen, they are frequently uploaded with further information on the host (which animal the pathogen was obtained from), where and when it was obtained, and who by. EID2 takes this information, and draws conclusions; for example, that a certain type of pathogen infects a certain host species, and is/was present in a certain country at a certain time. Similar conclusions can be drawn, and added to EID2, from the tens of millions of publications held in other public databases, thereby covering times and places where sequencing has not been extensive. EID2 can map the pathogens and, using incorporated climate data, it can model the climate conditions that determine their distribution. EID2 is open access.
TRDF funding will enable us to finalise the development of EID2 into a tool and resource for researchers of pathogens of livestock and domestic pets. We will develop the database to hold more spatially detailed information (at county rather than country level) and improve its ability to handle records where the host species is not clearly defined. We will add further environmental data to allow users to produce better models to explain pathogen distributions, and even predict them in the future, given climate change; and we will allow users to work at the level of diseases, rather than individual pathogens or groups of pathogens. Finally, we will give users the ability to add certain information of their own.

This proposal aims to improve a new open-access database of livestock (and other) pathogens, called EID2 (ENHanCED Infectious Diseases 2). EID2 has been built by bringing together information from tens of millions of records held in the NCBI's publicly-accessible taxonomy, nucleotide and Pubmed databases. The database provides, we believe, the most complete list of animal (including human) pathogens. It is taxonomically structured, meaning it is possible to select information for higher taxonomic levels such as genera, families etc. It is spatial, storing and mapping the countries of presence for thousands of pathogens; and it uses an evolutionary machine learning technique to analyse the climatic conditions associated with pathogen presence.
TRDF funding will enable us to finalise the development of EID2 into a tool and resource for researchers of pathogens of livestock and domestic pets. We will develop the database to hold more spatially detailed information (at county/state/province rather than country level) and improve its ability to extract information from records where the host species is ambiguous. We will add further environmental data to allow users to produce better models to explain pathogen distributions, and predict them in the future, given climate change; and we will allow users to work at the level of diseases, rather than individual pathogens or groups of pathogens. Finally, we will add crowd-sourcing functions that will give users the ability to add certain information of their own, such as nominating new associations (host-pathogen; pathogen-country) or correcting mistaken entries.

Infectious diseases of livestock are, to varying extents, the business of a large number of non-academic organisations: from government ministries and international organisations concerned with animal health (e.g. OIE) and food security (FAO), to NGOs concerned with development, and charities concerned with natural disasters. Concerning government, the greatest relevance is (in the UK) the Department for Food and Rural Affairs and its agency, AHVLA, but livestock diseases also touch on the Department of Health (Zoonoses), Department for Business, Innovation and Skills (commercial opportunities, economic costs), and the Ministry of Defence (bioterrorism). This broad relevance is demonstrated to some extent by the range of organisations which have commissioned livestock-centred reports from Baylis in recent years: the UK government's Foresight programme (2005), the Health Protection Agency (2010), the World Bank (2011), the US Department of Defense (2011) and the Smith School of Enterprise and the Environment (2011).
We believe government and other organisations can already or will shortly be able to use EID2 for the purposes of horizon scanning (for pathogens near to Europe, or present in specific trading countries, or most sensitive to climate), for information gathering in order to prepare briefings for government (on specific pathogens during an emergency or potential emergence event), or as a research tool for policy development for disease control. Longer term, it may serve a function in terms of disease surveillance (EID stores both time and space information), although its dependence on publications and sequence uploading means it cannot be, and is not intended to be, as responsive as ProMed for example.