The Infectious Diseases of East African Livestock (IDEAL) Project Database - Stable Snapshot

The Infectious Diseases of East African Livestock (IDEAL) project was a longitudinal cohort study of calf health which was conducted in Western Kenya between 2007-2009. It collected information on 548 East African shorthorn zebu calves and followed them for the first year of life. Blood and tissue samples were collected in association with all visits and screened using a range of laboratory based diagnostic methods for over 100 different pathogens or infectious exposures. This comprehensive dataset, the bio-repository of all the data and samples collected by the project, the metadata and the protocols for the study can be accessed through the IDEAL database website which has extensive filtering and searching capabilities. The database is evolving as new diagnostic tests are carried out on the bio-bank samples. Here we provide a stable copy snapshot of the IDEAL database at the time of publication in the form of raw CSV files to ensure long term storage of the data. The development of the forward-facing open-access IDEAL database was funded in part by the Bill & Melinda Gates Foundation and with UK aid from the UK Government’s Department for International Development (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland’s Rural College), and the International Livestock Research Institute. The original IDEAL project was funded by Wellcome Trust (grant No. 079445). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government. Here we provide a stable copy of the IDEAL database in the form of raw CSV files to ensure long term storage of the IDEAL project data. As new diagnostic tests are carried out on the bio-banked samples, we will update the IDEAL project website and database. The data presented here represents a snapshot of the database at the time of publication. A full description of the data in the related IDEAL database paper and on the IDEAL project website, along with the latest version of the database. Briefly, the data presented here contain the following information: Data Dictionary (data_dictionary.csv): Contains a description of the data in each column of the tables. Farm information (ideal_farm.csv): Contains all the farm level information which was collected at the recruitment visit using the main household questionnaire. This includes details about the farm, type of animals kept and animal husbandry and management practices. There is only one row per calf in this table as only one calf was recruited per farm, so in total this table consists of 548 rows. To comply with the General Data Protection Regulation (EU GDPR), all the information collected on the farmer during the main household questionnaire has been removed from this publication. Calf information (ideal_calf.csv): Contains the information about the calf. This includes information about the calf at each visit, this includes subjective assessments of the calf health, body condition score, weight and girth measurements, rectal temperature, presence of ectoparasites as well as movement in and out of the herd between visits and illnesses within the herd. There is one row per visit in this table, as each calf received multiple visits. This means that static phenotypic information such as coat colour and horn profiles is repeated for each calf across these visits. Therefore, there are 5641 rows in this table, consisting of 5337 routine visits, 216 clinical visits and 88 post-mortem visits for the 548 calves. Dam information (ideal_dam.csv): Contains all the information about the dam. This includes information about the dam at each visit, subjective assessments of the dam’s health, body condition score, girth measurements, ‘California Mastitis Test’ results and disorders of the udder areas. As with the calf data, there is one row per visit in this table, as each dam received multiple visits until the calf was weaned. There are 5044 rows in this table. Static phenotypic information such as coat colour and horn profiles is repeated for each dam across these visits. Test information (ideal_test.csv): Contains results of all the diagnostic tests including haematological profiles carried out on blood and other samples from the calves and dams at each visit so there are multiple rows per visit per calf. Clinical information (ideal_clinical.csv): Contains information on all the clinical episodes the calf experienced. This table includes information on the body part affected by the disorder, the disorder/lesion and the extent of the lesion. Post-mortem information (ideal_postmortem.csv): Provides detailed information on the cause of death for each of the 88 calves which died as gathered by the post-mortem reports. Sample information (ideal_sample.csv): Links the samples taken at each visit to the samples stored in the bio-bank. Follow-up study (ideal_followup.csv): A year after the final visit was made to the IDEAL cattle, a follow-up questionnaire was carried out asking about the status of the calf and whether or not it had offspring. This follow-up information is contained within this table. Genetic information: The IDEAL cattle were genotyped with the Illumina BovineSNP50 BeadChip v. 1 and the Illumina BovineHD Genotyping BeadChip. The BovineSNP50 data are contained within the standard format PLINK .ped and .map files and can be linked to the IDEAL data directly using the sample IDs provided (ideal_50K_snp.ped and ideal_50K_snp.map). The BovineHD is contained within the .map and .txt files and can be related to the IDEAL cattle using the SampleID to CalfID.csv file (ideal_770K_snp.txt; ideal_770K_snp.map and ideal_770K_snp_sampleid_calfid.csv). In all tables, a unique identification code has been assigned to the data records to facilitate the tracking of data. This unique identification system allows the application user to link the calf to its dam and farmer as well as back to its visit and sample or test result. The identification system does not relate to any other identification system other than that created by IDEAL project. For more information on linking tables see the IDEAL project website or the related IDEAL database paper. A full description of the IDEAL project design can also be found in: Bronsvoort et al. 2013. Design and descriptive epidemiology of the Infectious Diseases of East African Livestock (IDEAL) project, a longitudinal calf cohort study in western Kenya. BMC Vet Res 9, 171. DOI:10.1186/1746-6148-9-171 A full description of the IDEAL database can be found at: Callaby et al. unpublished. The Infectious Diseases of East African Livestock (IDEAL) Project Database. Nature Scientific Data The IDEAL database and website can be found at: data.ctlgh.org