There is great interest in producing dairy cows that are healthy and remain in the herd longer. Direct and indirect costs associated with disease represent a significant expense to producers, and selection for improved health may reduce these costs significantly. Genetic response to selection for improved health based upon breeding values from genetic evaluations of field-recorded traits has been well-documented. That genetic variation is not currently being directly utilized for genetic improvement. Standardized health event codes and a data exchange format (Format 6) for the collection of data from on-farm record-keeping systems are necessary for the creation of a national database for health data.

1. A data exchange format and national database for producer-recorded
health event data from on-farm management software
J. B. Cole, D. J. Null*, and L. R. Bacheller
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
Abstract T6
A Format 6 record includes detailed cow identification, a
health event code, an event date, and an optional detail field
(Figure 1). This format can provide the necessary data for
research into, and implementation of, genetic evaluations for
economically-important health traits. Format 6 was designed to
be easily extensible, as demonstrated by the addition of a
locomotion score event to the specification in July, 2008.
The existing table of lactation data, which is used to store
lactation information and test day yields, was modified to
include health event data transmitted on Format 6. Records
are indexed using a composite key constructed from a unique
internal animal ID, the calving date initiating a lactation, and
the ID for the herd in which the record was initiated. Each
record includes two columns associated with health data, an
integral event counter and a variable-length string (VARCHAR)
that contains the health event segments. Test day (Format 4)
and reproductive (Format 5) data are stored in the national
dairy database using the same strategy.
Incoming Format 6 records are processed nightly using a
sophisticated system of edits designed to insure data quality
and consistency (Wiggans and Thornton, 2008). When problems
are detected in the incoming data detailed error messages are
generated for use by the dairy records processing centers.
Record and Database Structure
Dairy Records Management Systems (Raleigh, NC)
provided about 3.7 million producer-recorded health events
for 1,834 herds from 1997 through 2003. Records included cow
ID, date, health event code (4-character), and a comment field
(up to 16 characters of supplemental information). A herd-
based dataset included codes used by each farm with a 12-
character code definition. The herd and event datasets were
merged, and standardized codes were assigned to the events.
Of the event records, 34% were categorized as health
events and 59% as health maintenance or management events
(e.g. vaccinations, hoof trims not associated with lameness,
dry treatments, etc.). Only health disorders were retained.
Introduction
There is great interest in producing dairy cows that are
healthy and remain in the herd longer. Direct and indirect costs
associated with disease represent a significant expense to
producers, and selection for improved health may reduce these
costs significantly. Genetic response to selection for improved
health based upon breeding values from genetic evaluations of
field-recorded traits has been well-documented. That genetic
variation is not currently being directly utilized for genetic
improvement. Standardized health event codes and a data
exchange format (Format 6) for the collection of data from on-
farm record-keeping systems are necessary for the creation of
a national database for health data.
Discussion
The potential for improvement of dairy cattle health by
means of genetic selection has been well-documented (Lyons
et al., 1991; Zwald et al., 2004). However, health traits
generally have low heritabilities, which means that large
numbers of high-quality data are needed to produce accurate
breeding value estimates. Format 6 provides a way for
processing centers to transmit health event data to AIPL for
research, but considerable work remains to convince producers
that it is worthwhile to contribute their data. An even greater
challenge may be that of encouraging software vendors to use
the Format 6 codes in their on-farm applications.
In this study, data were carefully inspected and records
were assigned to standardized categories. This process must be
automated for routine use, but the fact that producers can
define their own codes in the on-farm software presents a
significant challenge. The dataset of 3.7 million records from
DRMS included over 2,600 different event codes, including 42
different codes related to diagnosis and treatment of lameness.
These results, as well as the experiences of Zwald et al.
(2004), underscore the desirability and difficulty of assigning
standardized codes to current health event data.
The results of this study show that it is feasible to collect
health event data from on-farm management systems and
combine them with other cow data in a national database.
Further research is needed to determine how best to use those
data to improve the health of dairy cows.
References
Animal Improvement Programs Laboratory. 2006. Format 6.
http://aipl.arsusda.gov/formats/fmt6.html. Accessed 26
June, 2008.
Lyons, D. T., A. E. Freeman, and A. L. Kuck. 1991. Genetics of
health traits in Holstein cattle. J. Dairy Sci. 74:1092—
1100.
Wiggans, G. R., and Thornton, L. L. M. 2008. Processing of data
discrepancies for U.S. dairy cattle and effect on genetic
evaluation. Proc. Intl. Committee Anim. Recording,
Niagara Falls, NY, June 16, pp. 19—24.
Zwald, N. R., K. A. Weigel, Y. M. Chang, R. D. Welper, J. S.
Clay. 2004. Genetic selection for health traits using
producer-recorded data. I. Incidence rates, heritability
estimates, and sire breeding values. J. Dairy Sci. 87:4287
—4294.
Standard Health Event Codes
Testing
The database and editing systems were tested by
processing actual health event records provided by two dairy
records processing centers, DRMS and AgSource Cooperative
Services (Verona, WI). AgSource provided 1,285 lactation
records and included 1,585 distinct health events. The DRMS
data included 63,423 health events from 23,332 lactations.
The most frequent reported events differed by center and
did not overlap. AgSource herds most frequently reported
diarrhea (23%), ketosis (11%), lameness (11%), and teat injury
(21%). The DRMS herds reported mastitis (38%), metritis (16%),
and other reproductive problems (15%) most often. These
differences may be related to software: AgSource herds
typically use DairyCOMP 305™ (Valley Agricultural Software,
Tulare, CA), while DRMS herds usually use PCDART™.
AgSource DRMS
Health Event Records % Records %
Cystic Ovary 147 9 2,325 4
Diarrhea 355 23 99 <1
Digestive Problem — — 1,867 3
Displaced Abomasum 124 8 798 1
Downer Cow — — 46 <1
Dystocia — — 1,515 2
Johne’s Disease — — 519 1
Ketosis 176 11 2,373 4
Lameness 167 11 2,666 4
Mastitis — — 23,927 38
Metritis — — 10,141 16
Milk Fever 58 4 553 1
Reproduction 115 7 9,616 15
Respiratory Problem 74 5 1,839 3
Retained Placenta 48 3 4,867 8
Teat Injury 326 21 156 <1
Udder Edema — — 114 <1
Total 1,545 100 63,423 100
Standard codes for 19 health and 3 management events
were developed based on the frequency of events in the DRMS
data and consultation with veterinary experts. The most
frequent health events were mastitis (19%), lameness (5%),
metritis (5%), cystic ovary (3%), and retained placenta (2%).
Format 6 includes management traits for ease of collection,
and because they may be associated with longevity and
profitability.
Eighteen AgSource events had errors, which were event
dates later than the processing date (16%), records with no
production data (68%), and differing herd IDs for health and
yield data (16%). A total of 3,920 DRMS events had errors, the
most common of which were calving dates that did not match
event dates for dystocia (26%) and calving dates with no
matching test day data (72%).
Health Events
Cystic Ovary Metritis
Diarrhea/Scours Fever/Hypocalcemia
Digestive Problem/Off Feed Nervous System Problem
Displaced Abomasum Other Reproductive Problem
Downer Cow Respiratory Problem
Dystocia Retained Placenta
Johne’s Disease (clinical) Stillbirth/Perinatal Survival
Ketosis/Acetonemia Teat Injury
Lameness Udder Edema
Mastitis (clinical)
Management Events
Body Condition Score Milking Speed
Temperament