A data format is needed to facilitate the collection and exchange of health events for research by AIPL based on information available through the Dairy Herd Improvement program. This document describes the format for health records and is compatible with AIPL Format 4 (Lactation Record) and Format 5 (Reproductive Record).

Format 6 is identical to format 5 through byte 137. Like format 5, a number of health event segments may be stored in each record. A format 6 record begins with a calving event and ends prior to a subsequent calving or with the disposal of an animal. Heifer records will be handled in the same manner as reproductive events. For a heifer, the calving date will be blank. A heifer record will capture all health events prior to the first calving.

Format 6 can capture not only disease incidence, but also disease severity information when it's available. A two-level system is proposed for describing health events and consists of the health event code and the health event detail (optional). The format is designed to record disease incidence data rather than disease or preventative treatment data.

Following the system used for test-day and reproductive event data, up to 20 events may be reported per format 6 record, and multiple format 6 records may be reported per lactation. All health events for which codes have been defined should be forwarded in format 6 records. Events for which a code has not been defined will not be stored.

Descriptions and four-character codes for the health events to be reported are presented below. Diseases were selected for inclusion in format 6 based on an analysis of events reported in field data, as well as on their frequency of occurrence and economic impact as reported in the literature. Format 6 is an extensible format and additional health event codes can be defined as necessary to accommodate future needs. The four-character codes are for data transmission purposes and do not need to be made visible to the user of the on-farm management system.

Description

Standard Code1

Usage Notes2

Health Traits
Cystic Ovary	CYST	N
Diarrhea/Scours	DIAR	N
Digestive Problem/Off Feed	DIGE	Y
Displaced Abomasum	DA--	N
Downer Cow	DOWN	Y
Dystocia	DYST	Y
Johne's Disease/Paratuberculosis	JOHN	Y
Ketosis/Acetonemia	KETO	N
Lameness	LAME	Y
Leukosis (bovine leukemia virus)	LEUK	Y
Mastitis (clinical)	MAST	Y
Metritis	METR	N
Milk Fever/Hypocalcemia	MILK	N
Nervous System Problem	NERV	Y
Reproductive problem other than CYST, DYST, METR, RETP	REPR	N
Respiratory Problem	RESP	Y
Retained Placenta	RETP	N
Stillbirth/Perinatal Survival	STIL	Y
Teat Injury	TEAT	N
Udder Edema	EDEM	N

Management Traits
Body Condition Score	BCS-	Y
Locomotion Score	LOCO	Y
Milking Speed	SPEE	Y
Temperament	TEMP	Y

Control Codes
Delete records for the specified health event date	DELE	N

1 Hyphens ('-') are used to indicate empty columns when an event code is less than 4 bytes. Those columns should be filled with blanks (spaces) in files sent to AIPL.
2 N = No additional information is provided in the "Usage Notes"; Y = Additional material, such as the format and contents of the Health Event Detail field, is described in the "Usage Notes" below.

Dystocia and stillbirth data are currently received by AIPL in a separate format from lactation and reproductive records. Inclusion of these traits may lead to improved reporting and improve our ability to accurately model the impact of dystocia and stillbirth on production. These data will complement, rather than replace, data currently collected for these traits.

Abortions are not included in format 6 because they are already captured in format 4.

Body Condition Score
The health event detail field must contain the body condition score to two decimal places multiplied by 100, e.g. 2.00 would be reported as 200 and 3.25 as 325. Valid body condition scores range from 1 to 5, and valid scores in the BCS event detail field range from 100 to 500. The health event detail field for a BCS record has the following format:

Detail	Pos	Num Bytes	Values
Body condition score	1-3	3	200, 325, etc.
Reserved for future use	4-6	3	blanks

See "Sample Health Event Segments".

Digestive Problem/Off Feed
A cow that is off feed should be classified as DIGE only when no other disease is present, e.g., a cow that is off feed because of lameness should be classified as LAME rather than as DIGE. If a cow is known to be affected by both a digestive problem, such as bloat, and a specific disease or health problem, segments may be provided for both events.

Downer Cow
If a downer cow is known to be affected by a specific disease or health problem, records may be provided for both events. For example, if a cow has a difficult calving and then goes down, both DOWN and DYST segments may be reported.

Dystocia
The number of calves, followed by the calving ease score, must be recorded in the health event detail field. Calving ease scores should be provided for all births, regardless of difficulty, rather than scores only for difficult births. Scores should be assigned using the five-point scale: 1 = No problem; 2 = Slight problem; 3 = Needed assistance; 4 = Considerable force; 5 = Extreme difficulty. The health event detail field for a DYST record has the following format:

Detail	Pos	Num Bytes	Values
Number of calves born	1	1	1-3
Calving ease score	2-4	1-3	1-5 (one score per calf born)
Reserved for future use	3/4-6	2-4	blanks

See "Sample Health Event Segments".

Johne's Disease (Paratuberculosis)
A number of different diagnostic tests may be used to test for Mycobacterium paratuberculosis, including ELISA, fecal culture, and PCR-based tests. Event details include the type of test used, the associated test score, and the diagnosis assigned by the laboratory performing the test.

Detail	Pos	Num Bytes	Values
Diagnostic test	1	1	G, I, L, O, P, R, or S
Score	2/none	1–4/none	000 to 400 (raw score × 100) for type G, zero-filled; 0000 to 1000 (raw score × 100) for type I, zero-filled; 00 to 42 for type L, zero-filled; No score is reported for type O; 000 to 420 ([raw score + 0.20] × 100) for type P, zero-filled; 00 to 44 for type R, zero-filled; 0000 to 0300 or TNTC (too numerous to count) for type S, zero-filled
Johne's status	2–6	1	P for positive and N for negative
Reserved for future use	3–6/none	1–4/none	blanks

Diagnostic test The type of diagnostic test used is indicated by a one-character code assigned as follows: Code Test type Reference (website) G Fecal PCR (gel-based) – I IDEXX Laboratories Mycobacterium paratuberculosis test kits IDEXX Laboratories L Fecal culture (liquid media) – O Other test (histology, acid fast stain, etc.) – P ParaCheck® milk ELISA Prionics R Fecal PCR (real-time) – S Fecal culture (solid media) –

NOTE: Mention of specific product names does not constitute an endorsement on the part of the United States Department of Agriculture.

See "Sample Health Event Segments".

Lameness
Codes used to distinguish between lameness due to infectious pathogens (I), lameness due to metabolic causes (M), and lameness due to physical trauma (T), may be provided in the detail filed. A record for a cow with lameness attributable to hairy heel wart will receive the health event code LAME and may include the notation "I" in byte 1 of the health event detail field. The health event detail field for a LAME record has the following format:

Detail	Pos	Num Bytes	Values
Cause of lameness	1	1	I, M, T, blank
Reserved for future use	2-6	5	blanks

See "Sample Health Event Segments".

Leukosis
Several different diagnostic tests may be used to test for the presence of bovine leukemia virus (BLV), including three ELISA-based tests and an immunidiffusion test. Event details include the type of test used, the associated test score, and the diagnosis assigned by the laboratory performing the test.

Detail	Pos	Num Bytes	Values
Diagnostic test	1	1	A, I, S, or V
Score	2	3	000 to 900 (raw score × 100) for all tests, zero-filled;
BLV infection status	5	1	P for positive, S for suspect, and N for negative
Reserved for future use	6	1	blanks

Diagnostic test The type of diagnostic test used is indicated by a one-character code assigned as follows: Code Test type Reference (website) A AntelBio ELISA AntelBio I IDEXX Laboratories Bovine Leukemia Virus/Enzootic Bovine Leukosis test kits IDEXX Laboratories S Synbiotics Leucose Bovine AGID Synbiotics Corporation V VMRD Bovine Leukemia Virus Antibody Test Kit VMRD, Inc.

NOTE: Mention of specific product names does not constitute an endorsement on the part of the United States Department of Agriculture.

See "Sample Health Event Segments".

Locomotion Score
Scores may be provided on either the 6-point scale of Hernandez et al. (2007) (H) or the 5-point scale of Sprecher et al. (1997) (S).

Detail	Pos	Num Bytes	Values
Type of scale	1	1	H or S
Cow's locomotion score	2	1	1–6 for type H; 1–5 for type S
Reserved for future use	3–6	4	blanks

See "Sample Health Event Segments".

Mastitis (clinical)
The health event detail field for MAST events will store information on affected quarters, clinical appearance, and organisms. A separate health event segment should be generated for each infected quarter. Organisms should only be indicated when confirmed by a culture. The health event detail field for a MAST record has the following format:

Detail	Pos	Num Bytes	Values
Affected quarter	1-2	2	FL, FR, RL, RR, blank
Clinical appearance	3	1	1, 2, 3, blank
Organism	4	1	A, B, C, E, K, M, N, O, P, R, S, Y, blank
Reserved for future use	5-6	2	blank

Affected quarter The affected quarted is indicated by a two-character code where the first character is "F" for front or "R" for rear and the second character is "L" for left or "R" for right.

Clinical appearance Clinical appearance is indicated by a one-character code assigned as follows: Code Appearance 1 Quarter has abnormal milk, quarter is not swollen or inflamed, cow is not sick 2 Quarter has abnormal milk, quarter is swollen or inflamed, cow is not sick 3 Quarter has abnormal milk, quarter is swollen or inflamed, cow is sick

Organism Organisms are indicated using a one-character code. Organisms are only identified when the quarter has been cultured. When no culture has been taken, a blank should be assigned to this byte. Organism1 Code Corynebacterium bovis B Escherichia coli E Klebsiella spp. K Mycoplasma spp. M Psuedomonas aeruginosa P Staphylococcus aureus R Staphylococcus spp. (other than S. aureus) C Streptococcus agalactiae A Streptococcus spp. (other than S. agalactiae) S Yeast Y Other organism O No culture taken blank No growth on cultured plate N 1spp. = species

See "Sample Health Event Segments".

Milking Speed
Either scores on an ordered scale or actual milking times must be provided. The type of measurement is specified in byte 1 of the health event detail field as "O" for an ordered scale and "T" for an actual time. The format of SPEE detail records differs according to the type of measurement used:

Ordered Scale ("O") Detail	Pos	Num Bytes	Values
Type of scale	1	1	O
Points on scale	2-3	2	01-99, zero-filled
Cow's milking speed	4-5	2	01-99, zero-filled, <= Points on scale value
Reserved for future use	6	1	blank

Time ("T") Detail	Pos	Num Bytes	Values
Type of scale	1	1	T
Actual milking speed	2-5	4	Time (MM:SS) with no separator, zero-filled
Reserved for future use	6	1	blank

Due to the lack of an industry-standard scale, the number of points on "O" scales must be provided, as well as the cow's milking speed on that scale. Ordered scales are assumed to begin with 1. The mean is assumed to lie in the middle of the range (e.g. 5 on a 9-point scale), with values larger than the mean corresponding to shorter milking times (faster speeds) and values smaller than the mean corresponding to longer milking times (slower speeds). Actual milking times are reported in minutes and seconds. Note that no separator between minutes and seconds should be included in bytes 2-5 of an actual time ("T") record. Multiple-byte numeric fields should be zero-filled. See "Sample Health Event Segments".

Nervous System Problem
Symptoms of nervous system problems include staggering, circling, head tilting, paralysis, and coma.

Respiratory Problem
This trait include pneumonia and all other observed respiratory problems.

Stillbirth/Perinatal Mortaility
The number of calves born, and a stillbirth score for each calf, must be recorded in the health event detail field. Stillbirth scores should be provided for all births rather than scores only for stillborn calves. Scores should be assigned using the three-point scale: 1 = Calf alive 48 hours after birth; 2 = Calf was born dead; 3 = Calf was born alive but died within 48 hours of birth. The health event detail field for a STIL record has the following format:

Detail	Pos	Num Bytes	Values
Number of calves born	1	1	1-3
Stillbirth score	2-4	1-3	1-3 (one score per calf born)
Reserved for future use	3/4-6	2-4	blanks

See "Sample Health Event Segments".

Temperament
A cow's termperament must be scored and reported on an ordered scale, much like the "O" type of milking speed measurement. Scales are assumed to begin with 1. The mean is assumed to lie in the middle of the range (e.g. 5 on a 9-point scale), with values larger than the mean corresponding to more desireable temperaments and values smaller than the mean corresponding to less desirable temperaments. Multiple-byte numeric fields should be zero-filled. The health event detail field for a TEMP record has the following format:

Detail	Pos	Num Bytes	Values
Points on scale	1-2	2	01-99, zero-filled
Cow's temperament	3-4	2	01-99, zero-filled, <= Points on scale value
Reserved for future use	5-6	2	blanks

See "Sample Health Event Segments".

Sample health event segments are provided to demonstrate proper usage. Only bytes 138+ of each segment are presented. Hyphens ('-') are used to indicate empty fields which should be filled with blanks (spaces) in files sent to AIPL.

Body Condition Score

An animal with a body condition score of 3.25 indicated in the health event detail field. (note that the decimal point is not stored)

BCS-20031004A325---

Dystocia

A single birth with a calving ease score of "1" indicated in the health event detail field

DYST20031004A11----

A twin birth with a calving ease score of "3" indicated in the health event detail field note that a calving ease score is provided for each calf born)

DYST20031004A233---

Johne's Disease (Paratuberculosis)

A Johne's-free sample based on a fecal gel-based PCR score of 0.05. The score reported in the Format 6 record is calculated as: 0.05 × 100 = 05.

JOHN20090604AG005N-

A diagnosis of Johne's disease based on a raw score of 0.25 on an IDEXX ELISA test. The score reported in the Format 6 record is calculated as: 0.35 × 100 = 35. Note that the four-byte score is zero-filled, so 35 is coded as 0035.

JOHN20090604AI0035P

A diagnosis of Johne's disease based on a score of 7 from a liquid-media fecal culture. Note that the two-byte score is zero-filled, so 7 is coded as 07.

JOHN20090604AL07P--

A diagnosis of Johne's disease based on an unspecified test. This corresponds to the definition of the JOHN event type used in drafts of Format 6 prior to June, 2009.

JOHN20090604AOP----

A sample positive for Johne's disease based on a raw score of 0.20 on a ParaCheck© milk ELISA test. The score reported in the Format 6 record is calculated as: (0.20 + 0.20) × 100 = 40. Note that the three-byte score is zero-filled, so 30 is coded as 040.

JOHN20090604AP040P-

A real-time fecal PCR test resulting in a diagnosis of Johne's disease. Note that the two-byte score is zero-filled, so 9 is coded as 09.

JOHN20090604AR09P--

A diagnosis of Johne's disease based on a fecal culture on solid media. Note that the four-byte score is zero-filled, so 85 is coded as 0085.

JOHN20090604AS0085P

Lameness

Lameness caused by an infectious agent, such as hairy heel wart

LAME20031004AI-----

Lameness with no reported cause

LAME20031004A------

Leukosis

A positive diagnosis of leukosis (bovine leukemia virus) based on a raw score of 0.6 on an AntelBio Leukosis Milk ELISA test. The score reported in the Format 6 record is calculated as: 0.6 × 100 = 600.

LEUK20101020A600P0

Locomotion Score

A locomotion score of 4 (lame – an arched-back posture is always evident, gait is best described as one deliberate step at a time, and one or more feet/limbs are favored) on the scale of Hernandez et al. (2007).

LOCO20090414AH4----

A locomotion score of 1 (the cow stands and walks with a level-back posture and her gait is normal) on the scale of Sprecher et al. (1997).

LOCO20090414AS1----

Mastitis

A three segment case of clinical mastitis in the right front quarter, the quarter is inflamed but the cow is not sick, and the organism was cultured as Staphylococcus aureus

MAST20041001AFR2R--

MAST20041002AFR2R--

MAST20041004AFR1R--

Milking Speed

A cow with faster than average milking speed (7) on a 9-point scale

SPEE20031004AS0907-

A cow that took 10 minutes and 30 seconds of actual time to milk out

SPEE20031004AT1030-

Stillbirth/Perinatal Survival

A single birth with a live calf 48 hours postpartum

STIL20031004A11----

A twin birth with one stillborn calf and one live calf 48 hours postpartum

STIL20031004A221---

Temperament

A cow with an average temperament score (5) on a 9-point scale

TEMP20031004A0905--

A cow with a poor temperament score (undesirable) (10) on a 50-point scale

TEMP20031004A5010--

As noted above, Format 6 is designed to be an extensible format which can accommodate new traits as they are identified by the industry and support the expansion of current data collection efforts. Although it does not report service sire ID information, which can be reported using Format 5 (Reproduction Record), Format 6 can be used to report dystocia and stillbirth scores. As software support for collecting health and reproductive data improves, the NAAB calving ease format can be replaced with Formats 5 and 6, which would simplify collection of data for the NAAB calving traits program.

Hernandez, J., J. Shearer, C. Risco, and W. Thatcher. 2007. Lameness and reproductive performance in dairy cows. Pages 109–113 in Proc. Dairy Cattle Reprod. Conf., Denver, CO.

Sprecher, D. J., D. E. Hostetler, J. B. Kaneene. 1997. A lameness scoring system that uses posture and gait to predict dairy cattle reproductive performance. Theriogenology 47:1179–1187.