Interbeef Guidelines

Version 1
InterBeef

contact: Interbull Centre - Dept. Animal Breeding and Genetic SLU,
Box 7023 S-75007 Uppsala, Sweden

Phone: 0046-18-671994
Fax: 0046-18-672848
E-mail : interbeef@slu.se
URL : https://www.icar.org/index.php/technical-bodies/working-groups/interbeef-working-group/

Contents

Interbeef Guidelines
README for CheckPedigree.py
README for CheckLinks.py

1. INTRODUCTION

Countries willing to join InterBeef must be members of Interbull and support the ICAR guidelines for data collection (http://www.icar.org/). This document is a description of the necessary actions and relevant files required by a new country willing to join InterBeef.

2. THE ANIMAL INTERNATIONAL IDENTIFICATION

2.1 Format

A unique international identification for each animal is used in the international genetic evaluation system and will be referred to as the Animal International IDentification (AIID). The AIID is constructed using the Interbull rules (referred as Interbull format in the document) and its structure is:

Breed + Country + Sex + Identification number

The field ‘Breed‘ of the AIID refers to the breed of identification of the animal in its country of first registration (in most cases, the country of origin): 3 characters as defined in the Interbull Breed Codes, available at www.interbull.org (see Reference section).
The field ‘Country’ of the AIID refers to the country of first registration of the animal (in most cases, the country of origin): 3 characters or 3 digits number as defined in ISO 3166 Codes, available at http://userpage.chemie.fu-berlin.de/diverse/doc/ISO_3166.html (see Reference section).
The field ‘Sex’ of the AIID refers to the sex of the animal (M = male ; F = female)
The field ‘Identification number’ of the AIID refers to the identification number of the animal in the country of first registration: 12 characters right justified with left blanks filled in with zero (“0”).

Ex: CHAFRAM006327826864 refers to

A Charolais CHA
First registered in France FRA
A male M
With the following identification in France 006327826864

Ex: BAQIRLF125693456875 refers to

A Blonde d’Aquitaine BAQ
First registered in Ireland IRL
A female F
With the following identification in Ireland 125693456875

2.2 Constructing the international identification number

A country should first construct the international identifications for the animals born on its soil. The general rule for this construction would be that a given identification number is unique within a country and a breed.

When an animal (live animal or issued from AI straw or embryo) is sold abroad, the importing country should avoid re-registration; in case of re-registration the original ID and the national ID should be kept.

The animal ‘IE231112150014’ is, for example, a pure breed Irish limousine female named ‘SHRIFFTOWN RIPPER’. Ireland has constructed its AIID as followed: LIMIRLF231112150014.

The animal ‘FR0384106449’ is a pure breed French Charolais bull named ‘VLADIMIR’. That animal is also used in Ireland under the name ‘VLADIMER’ and the number ‘0384106449’ and has also been re-codified ‘108376849’ and ‘VLR’. France constructs its AIID as followed: CHAFRAM000384106449.

In the international identification number, hyphens, slashes, commas, dots, blank spaces or any other symbols are allowed.

The animal ‘UK9373 70-2/-7’, for example, is a UK Salers female animal and its international identification number would be ‘SALGBRF9373 70-2/-7’

2.3 The New Web Interface at Interbull

Interbull has developed a new database, IDEA (Interbull Data Exchange Area) that allows register users to all the pedigree handling functionalities. IDEA is available at https://idea.interbull.org/

IDEA is exclusive for database users. To become a database user you need to belong to a national evaluation centre participating to the Interbeef evaluation. If you want to join the Interbeef evaluation and therefore have access to IDEA, your national genetic centre needs to be associated to a username and a contact email address. To get your national genetic centre listed among the ones participating to the Interbeef evaluation, you have to:

Send an email to interbeef@slu.se providing information on your national genetic centre: Full name and address of the organization and full name and email address of the designated contact person. Clearly state the breed(s) and trait(s) you wish to participate with. If your organization provides data as a joint evaluation including other countries, you clearly have to state for which other countries and breed(s) your organization provides pedigree and performance information.

Upon reception of your request, Interbull will send you by email a link to an IDEA-test environment together with a username and password so that you will be able to get acquainted with the IDEA functionalities and the user manual which is located under “Help”.

The national pedigree file must be first checked with the CheckPedigree.py script provided by Interbull Centre. The checking programs are available under “Software”. The zip files produced by the Python scripts represent the only valid infiles for the database; no other files will be accepted by the system.
When your pedigree enters the database it undergoes a series of checks called “verification process” aiming at identifying the correct authoritative organization of each and every animals listed in your pedigree. In general the system has been built in such a way that it accepts information only if these comes from the authoritative organization. Therefore, whenever you submit pedigree data, the system first checks that the combination “country-breed” in the animal ID matches with the combination your organization “owns”. If so the records are considered correct and stored in the database, if this is not the case then the records will be listed in the appropriate authoritative organization account waiting for verification, i.e. waiting for the authoritative organization to provide the correct pedigree information. In case the authoritative organization is a country or organization that does not yet participate to the Interbeef evaluation, then the animals will appear as verified by Interbull until eventually that country/organization would join the service.

Example:
Ireland submits the following pedigree records to the database:

601 CHAIRLM458962315289 CHAIRLM789456123652 CHAIRLF369852147852 1985 OMAR IRL
601 CHAFRAM865412398745 CHAFRAM231658479851 CHAFRAF845693274125 1988 OSCAR IRL

In the first case the animal is an Irish Charolais sent by Ireland. Ireland is therefore the authoritative organization for that animal so the record gets stored in the database. In the second case the animal appears to be a French Charolais sent by Ireland. Ireland is no longer the authoritative organization for this bull therefore the system will send the record to the French account and will wait for France to provide its correct pedigree information.

3. THE REQUIRED FILES

There are 5 groups of files to be created by a country willing to join the international beef genetic evaluation:

The 601 file representing the national pedigree file
The 602 file representing the national performance file (limited until now to adjusted weaning weights, adjusted carcass weight and calving ease)
The 603 file representing the parameter file.
The 604 file representing the ET file
The 605 file representing animals with official proof
The Beef Form, see Reference section.

A country willing to join InterBeef needs to include at least one breed and one trait in the process of the international genetic evaluation. The objective of the present document is to help a new member country in the construction of these files.

NB: Since the verification of the International ID is done via database, national cross-reference files are no longer needed. For more information about IID verification, please refer to the IDEA user manual.

3.1 General

3.1.1 The Different InterBeef steps

The construction of these files follows several steps:

The first step for a country that wishes to join the international evaluation system is to upload the pedigree file into the IDEA database (https://idea.interbull.org/).
Once the pedigree file (601) is uploaded into the database, the country will have to correct its own database according to the feedback obtained from the database regarding verified pedigree information from authoritative organizations. (see corrected foreign information in the IDEA user manual)
Once this step has been fulfilled then countries will create the performance file (file 602), parameter file (file 603) and eventually an ET file (file 604) either in xml format or flat files converted to xml format before checking these files and uploading it into the IDEA database (as described here https://wiki.interbull.org/public/IDEA_Beef_UserManual?action=print&rev=11)

3.1.2 General principles for file preparation:

Numeric information must be right justified.
Characters must be left justified.
All characters should be in upper case.

3.2 Fileformats

3.2.1 The national pedigree file (601 file)

3.2.1.0 General

The 601 file is a national pedigree file and must contain pedigree information of all animals included in the performance file in an animal-sire-dam format. Sires, dams and ancestors must also have an entry in this file as an animal; unknown ancestors should be coded ‘UUUUUUUUUUUUUUUUUUU’.

To ensure sufficient pedigree information it is recommended that pedigree information of animals born within a period equivalent to a minimum of three generation intervals should be included. The 601 file is a file issued per country or organization providing pedigree information according to the format shown in Table 1. The 601 files can contain one breed or multiple breeds.

3.2.2.1 Fileformat pedigree file

Table 1: 601 file format (total length = 107)

Field description	Label	Format	Start		Length		Status^a	Note	Example
Record type	RTYPE	Char		1		3	M		601
International ID of ANIMAL
Breed of the animal	ABREED	Char		5		3	M	I	LIM
Country of birth	AIDC	Char		8		3	M	II	FRA
Sex	ASEX	Char	11			1	M	III	F
ID code of the animal	AID	Char	12		12		M	IV	008795005065
International ID of Animal’s SIRE
Breed of the sire	SBREED	Char	25			3	O	I	LIM
Country of birth	SIIDC	Char	28			3	O	II	FRA
Sex	SSEX	Char	31			1	O	III	M
ID code of the sire	SIID	Char	32		12		O	IV	000095015085
International ID of Animal’s DAM
Breed of the dam	DBREED	Char	45			3	O	I	LIM
Country of birth	DIIDC	Char	48			3	O	II	FRA
Sex	DSEX	Char	51			1	O	III	F
ID code of the dam	DIID	Char	52		12		O	IV	001111001111
Additional information
Date of birth of animal	BDATE	Int	65			8	O	V		20010130
Name of animal	NAME	Char	74		30		O		Faust
Country sending information	RCOU	Char	105			3	M	II	FRA

^aStatus: M = Mandatory, O = Optional

Note
I	The field ‘Breed‘ of the AIID refers to the breed of identification of the animal in its country of first registration (in most cases, the country of origin): 3 characters as defined in the Interbull Breed Codes,
II	The field ‘Country’ of the AIID refers to the country of first registration of the animal (in most cases, the country of origin): 3 characters or 3 digits number as defined in ISO 3166 Codes, available at https://www.iso.org/obp/ui/#search
III	Sex : M for Male, F for Female only
IV	The field ‘Identification number’ of the AIID refers to the identification number of the animal in the country of first registration: 12 characters right justified with left blanks filled in with zero (“0”).
V	YYYYMMDD format

3.2.2 The performance file (602)

3.2.2.0 General

All animals with a performance must have a line as animal in the 601 pedigree file. The performance file must be constructed in agreement with the 601 file and be consistent with the international identification of the animal.
It is expected that countries participating with data support the ICAR guidelines for beef recording.
As indicated in the ICAR recommendations, any group of animals kept for the same purpose and at the same location shall be regarded as a whole herd. For a performance record to be considered an official record, the whole herd as defined above must be recorded. Each herd is identified with 15 digits identification, coded as characters:

The first three digits correspond to the country, using the ISO 3166 Alpha-3 system, see Reference section.
The next 12 digits correspond to the identification of the herd within the country. The original herd identification number should be used. The characters (letters or numbers) are right justified, the left blanks being filled with zeros.

All performance traits are associated with their environmental effects and complementary information (one observation line per measurement) as described in Table 2.

3.2.2.1 Special information for calving traits

Calving traits present a direct and a maternal component. For some traits, such as stillbirth and birth weight preparation of a file602 can be difficult because of the absence of an international ID for a dead calf. Given that Interbeef is an international data sharing platform, it is absolutely necessary that records are exchanged in a standardized way and that data quality must be ensured at the best of our capacity. Based on these two principles, there is a strong intention to keep phenotypic records under an universal formats capable of handling all possible traits (files 602 and 603). Likewise, only valid international animal idetification is admitted into the system (file 601).

Phenotypic records for calving traits will therefore be reported as maternal traits (the International ID of ANIMAL in the file602 will refer to the dam ID) with the necessary information to fit a model for the direct trait added in the "environmental effects" fields of file 602. This includes additional information about the calf, such as sire of the calf, sex of the calf, calf birth date and calf ID (when available). Consider, for instance a record for calving ease (cae). In file 602, a typical record could be reported as shown in Table 2 and in session "Examples performance and parameter files" - calving traits

When calf additional information is reported in File602 (Table 2), the equivalent parameter File603 should also refer to the same variables. Although calf additional information is reported in the "environmental effects" field, it is not necessarily intended to be fit as an effect into the statistical model for the maternal trait. Since records on file 602 refer do the CALF DAM, in the parameter file the type of effects refer to the model for the maternal trait only. Therefore, variables that are reported in File602 to be used in the direct trait model should be labeled as "C" in the effect type field, so it is clear they are not fixed or random effects, neither covariates in the maternal trait model.

In the example in session "Examples performance and parameter file" for calving traits, calf sex, parity, season and age at calving are included as a fixed effects (effect type "F" in File603), while calf sire, calf birthdate and calf ID are labelled as effect type "C", which means they will not be fitted in the maternal trait model, but used for modelling the direct effect. For instance, calf ID, calf sire and calf birthdate would be needed to create a pedigree structure for the direct trait analyses.

3.2.2.2 Fileformat performance file

Table 2: Performance file (602 file format – all fields are mandatory)

Field description	Label	Format	Starting byte	Ending byte	Field^a	Note	Example aww	Example cae
Record type	RTYPE	Char	1	3	3		602	602
Trait	FCODE	Char	5	7	3	I	AWW	CAE
Breed of evaluation	EBREED	Char	9	11	3	II	LIM	LIM
Country sending information	RCOU	Char	13	15	3	III	FRA	FRA
International ID							Referring to the animal itself	Referring to the dam of the calf
Breed of the animal	ABREED	Char	17	19	3	II	LIM	LIM
Country of birth	AIDC	Char	20	22	3	III	FRA	FRA
Sex	ASEX	Char	23	23	1	IV	F	F
ID code of the animal	AID	Char	24	35	12	V	008795005065	008795005065

Twinning	TWI	Int	37	37	1	VI	1	1
Embryo transfer	ET	Int	39	39	1	VII	0	1
Herd	HERID	Char	41	55	15	VIII	FRA000123456789	FRA000123456789
Dependent variable	Y	Int	57	66	10	IX	245	0
Number of environmental effects included in the national model	NENV	Int	68	70	3	XI	4	4
Environmental effect (n)^b	ENV(n)	Char	72		20	XII	2

^b Repeat this field n times (n = 1,…,NENV), adding one (1) empty space between fields; contemporary group should come as the first effect

Notes
I	See trait codes in Table 5 (abbreviations)
II	See Reference section for Breed codes
III	See Reference section for Country codes – ISO 3166 Alpha-3
IV	Sex : M for Male, F for Female only; U for unknown
V	Identification Number in Interbull Format : Alpha-numeric codes only, Right justified, Left blanks being filled with '0'
VI	1 = single birth ; 2 = twin birth
VII	0 = no ET ; 1 = ET Please note :For calving traits, the embryo transfer fleld in the 602 file is related the the calf and not the the dam itself.
VIII	Herd identification number corresponding to the herd included in the contemporary group. Format: 3 character country code + 12 digits
IX	Value observed for the trait in question. Ex: animal weaning weight ; 245 Kg (no decimals) calving traits; calf born dead =0;alive=1
XI	Defines the remaining number of fields in the record. Additional fields = NENV
XII	Value of the respective environmental effect for the current record. contemporary group (CG) should come as the first effect for both calving and weaning weight and then comes the trait specific env. effects Ex. Animal weaning weight env1=CG env2=Season (2(out of 4 classes)) env3= Birth weight (45 kg without decimals) env4=Sex of calf (1=M,2=F) Calving traits: env1=CG env2=Sire of the calf env3=Sex of the calf (1=M,2=F) env4=Calf birthdate YYYYMMDD env5=Calf id (if not available use UUUUUUUUUUUUUUUUUUUU) env6=Actual env. effect to be fitted in the model (Parity) env7= Actual env.effect to be fitted in the model (Age at calving) env 8= Actual env.effect to be fitted in the model (Season)

3.2.3 Parameter file (603)

3.2.3.0 General

The parameter file (603) contains the name of two variables and the names of the environmental effects for each trait included in the performance file (602). This file must be provided together with the 602 file.

3.2.3.1 File format parameter file

Table 3: Parameter file (603 file format) – one record per trait-breed combination (all fields are mandatory)

Field description	Label	Format	Starting byte	Field Length^a	Note	Example aww	Example cae
Record type	RTYPE	Char	1	3		603	603
Trait	FCODE	Char	5	3	I	AWW	CAE
Breed of evaluation	EBREED	Char	9	3	II	LIM	LIM
Country sending information	RCOU	Char	13	3	III	FRA	FRA
Reference age or class	REF	Int	17	5	IV	200	99999
Trait heritability	H2	Int	23	3	V	25	10
Minimum number of observation per CG	CGN	Int	27	10		5	5
Twins	TWIN	Char	38	1	VIII	Y	Y
Maternal (genetic) effect fitted in the model	DAM	Char	40	1	VIII	N	N
Maternal permanent environmental effect fitted in the model	MPE	Char	42	1	VIII	N	N
Permanent environmental effect fitted in the model	PEV	Char	44	1	VIII	Y	Y
Number of environmental effects included in the national model	NENV	Int	46	3	IX	4	7
Environmental effect (n)^b	ENV(n)	Char	50	20	X	HY	HYS
How ENV(n) is fitted in the model (type of effect)^b	ENVT(n)	Char	71	1	VII	F	F

^bRepeat these fields n times (n = 1,…,NENV), adding one (1) empty space between fields; contemporary group should come as the first effect

Notes


I	Use the trait codes in Table 5 (abbreviations)
II	See Reference section for Breed codes
III	See Reference section for Country codes – ISO 3166 Alpha-3
IV	Reference value (age or class) used to adjust the dependent variable. Ex. reference national weaning age = 200 days. For missing values use 99999.
V	Trait heritability used in the national evaluation, expressed in a scale from 1-100
VII	Describes if the effect should be fitted as a fixed effect, a random effect or as a covariable in the model. Use the type of effect codes in Table 4 (abbreviations) For calving : Variables that are reported in File602 to be used in the direct trait model should be labeled as "C" in the effect type field, so it is clear they are not fixed or random effects, neither covariates in the maternal trait model.
VIII	Declare if this specific effect (TWIN,DAM, MPE or PEV) is fitted into the national model (Y = yes; N = no)
IX	Defines the remaining number of fields in the record. Additional fields = 2*(NENV)
X	Describes the n^th environmental effect:Use the environmental effect codes in Table 5 (abbreviations). In case the trait is not yet included on Table 4, describe it briefly (20 characters) In case of polynomial effects, use the effect code followed by the order. Ex. (SEAS)² should be coded SEAS2 In case of interactions, combine the effect codes in the same field. Ex. (AAWG)*(ASEX) should be coded as AAWGASEX

Examples performance and parameter files

Animal weaning weight

Example performance file for aww:
602 AWW LIM CZE LIMCZEM000000181517 1 0 CZE008101626410        266   4                13118                    1                    3                 1995

The related paramter file (603) to the performance file (602) above should look like this:
603 AWW LIM CZE 210   11  1          N Y Y N 4   CG                  R ASEXTWIN             F Age_of_Dam           F Birth_Year           F

Explanation 602 file for aww:
602 = record type; AWW= trait; LIM=breed; CZE= country sending information; LIMCZEM000000181517=aid; 1=twin_info; 0=et_info ;CZE008101626410= herdid; 266=dependent_variable; 4= number of env. effects (should be the same as the number of env. effects in the parameter file (603);  13118=env. effect 1 which should be related to the env. effect 1 in the 603 file (in this case HYS), 1= env. effect 2 which should be related to the env. effect 2 in the 603 file (in this case ASEXTWIN); 3= env. effect 3 which should be related to env. effect 3 in the 603 file (in this case Age_of_Dam); 1995= env. effect 4 which should be related to the to env. effect 4 in the 603 file (in this case Birth_Year)

Explanation 603 file:
603 = record type; AWW=trait; LIM=breed; CZE= country sending information; 210=reference age or class; 11= trait heritability; 1= Minumum number of observations per CG; N=twin info; Y=Maternal (genetic) effect fitted in the model ; Y=Maternal permanent env. effect fitted in the model; N= Permanent env.effects included in the national model; 4= number of env. effects (should be same number as in the performance file 602); HYS=env.effect1 which is related to the env.effect 1 in the performance file; R= How env. effect is fitted into the model(type of effect); ASEXTWIN=env. effect2 which is realted to the env.effect 2 in the performance file; F=how env. effect nr 2 is fitted in to the model; Age_of_Dam=env.effect3 which is realted to env effect 3 in the performance file; F=how env. effect nr 3 is fitted in to the model; Birth_Year= env effect nr 4 which is related to the env effect 4 in the performance file; F=how env. effect nr 4 is fitted in to the model

Cavling traits

Example performance file for cae:
602 CAE LIM CZE LIMCZEF000000260705 1 0 CZE008101626410  1             8                 18256 LIMFRAM001984004136  1                    19950401
 LIMCZEM000000181517 1                    3                 1995

Explanation 602 file for cae:
602 = record type; CAE= trait; LIM=breed; CZE= country sending information; LIMCZEM000000181517=aid (referring to the dam of the calf); 1=twin_info(related the the calf); 0=et_info (related the the calf) ;CZE008101626410= herdid; 1=dependent_variable; 8= number of env. effects (should be the same as the number of env. effects in the parameter file (603);  18256=env. effect 1 which should be related to the env. effect 1 in the 603 file (in this case HYS), LIMFRAM001984004136= env. effect 2 which should be related to the env. effect 2 in the 603 file (in this case CASI); 1= env. effect 3 which should be related to env. effect 3 in the 603 file (in this case CSEX ==> 1=Male, 2=Female,3=Unknown); 19950401= env. effect 4 which should be related to the to env. effect 4 in the 603 file (in this case CABI); LIMCZEM000000181517 =env.effect 5 which should be related to env.effect 5 in the 603 file(in this case CAID ) ; 1= env. effect 6 which should be related to the env.effect 6 in the 603 file (in this case ASEXTWIN); 3=env.effect 7 which should be related to env.effect 7 in the 603 file(in this case Age_of_Dam); 1995 = env.effect 8 which should be related to env. effect 8 in the 603 file (in this case Birth_Year).

603 CAE LIM CZE 1     9   1          N Y Y N 8 CG           R  CASI                 C CSEX                 C CABI                 C CAID                 C ASEXTWIN             F Age_of_Dam           F Birth_Year           F
Explanation 602 file for cae:
603 = record type; CAE=trait; LIM=breed; CZE= country sending information; 1=reference age or class; 9= trait heritability; 1= Minumum number of observations per CG; N=twin info; Y=Maternal (genetic) effect fitted in the model ; Y=Maternal permanent env. effect fitted in the model; N= Permanent env.effects included in the national model; 8= number of env. effects (should be same number as in the performance file 602); HYS=env.effect1 which is related to the env.effect 1 in the performance file; R= How env. effect is fitted into the model(type of effect); CASI=env. effect2 which is realted to the env.effect 2 in the performance file; C=how env. effect nr 2 is fitted in to the model; CSEX=env.effect3 which is realted to env effect 3 in the performance file; C=how env. effect nr 3 is fitted in to the model; CABI= env effect nr 4 which is related to the env effect 4 in the performance file; C=how env. effect nr 4 is fitted in to the model; ASEXTWIN=env.effect nr 6 which is realted to the env.effect 6 in the performance file, F=how env. effect nr 4 is fitted in to the model;  Age_of_Dam=env.effect 7 which should be related to env.effect in the performance file; F=how env. effect nr 4 is fitted in to the model; Birth_year= env. effect 8 which is related to env.effect 8 in the performance file; F=F=how env. effect nr 4 is fitted in to the model

3.2.4 ET file (604)

3.2.4.0 General

The ET file (604) contains a list of ET IDs which will be included in the pedigree used for the international evaluation. Country willing to get international breeding values for ET animals based on parent average will have to provide the file at each evaluation. This file is not a mandatory file. Please note: For calving traits, the embryo transfer field in the 602 file is related the the calf and not the the dam itself.

3.2.4.1 File format ET file

Table 4: 604 file format (total length = 27) ET file

Field description	Label	Format	Start		Length		Status^a	Note	Example
Record type	RTYPE	Char		1		3	M		604
International ID of ANIMAL
Breed of the animal	ABREED	Char		5		3	M	I	LIM
Country of birth	AIDC	Char		8		3	M	II	FRA
Sex	ASEX	Char	11			1	M	III	F
ID code of the animal	AID	Char	12		12		M	IV	8795005065
Country sending information
Country	COU	Char	25			3	M	I	FRA

^aStatus: M = Mandatory, O = Optional

Note
I	See Reference section for Breed codes
II	See Reference Section for Country codes – ISO 3166 Alpha-3
III	Sex : M for Male, F for Female only
IV	Identification Number in Interbull Format : Right justified, Leading blanks filled with Zero (“0”)

3.2.5 OFCL file (605)

3.2.5.0 General

The OFCL file (605) contains a list of IDs of animals with official proof in the participating country. According to a new proposal for the publication policy, if the national proof of an animal is considered as official, the international predicted breeding value of the animal on the scale of that country would be publishable.

3.2.5.1 File format Official file

Table 5: 605 file format (total length = 31) Official file

Field description	Label	Format	Start		Length		Status^a	Note	Example
Record type	RTYPE	Char		1		3	M		605
International ID of ANIMAL
Breed of the animal	ABREED	Char		5		3	M	I	LIM
Country of birth	AIDC	Char		8		3	M	II	FRA
Sex	ASEX	Char	11			1	M	III	F
ID code of the animal	AID	Char	12		12		M	IV	8795005065
National reliability
Reliability	REL	Int	25		2				65
Status of bull	STATUS	Int	28		2		M	V	05
Country sending information
Country	COU	Char	31			3	M	II	FRA

^aStatus: M = Mandatory, O = Optional

Note
I	See Reference section for Breed codes
II	See Reference Section for Country codes – ISO 3166 Alpha-3
III	Sex : M for Male, F for Female only
IV	Identification Number in Interbull Format : Right justified, Leading blanks filled with Zero (“0”)
V	00 = unknown 05 = natural service bull (stock bull) 10 = bull randomly sampled through an official AI scheme 15 = young bull, genomically tested, not yet selected for AI use 20 = other bull, exclusion from International evaluation unless type of proof is “21” ( only dairy)

4. ABBREVIATIONS

Table 6: List of abbreviations used in Interbull files and documentation

	Type	Abbreviation	Meaning
1	General concepts	AI	Artificial Insemination
		ET	Embryo Transfer
		Kg	Kilogram
		MGS	Maternal Grandsire
		NS	Natural Service
		Ib	Pounds
2	Genetic evaluation methods	AM	Animal Model
		BLUP	Best Linear Unbiased Prediction
		FR	Fixed Regression
		MT	Multiple Traits
		RR	Random Regression
		RP	Repeatability (model)
		REML	Rextricted Maximum Likelihood
		ST	Single Trait
		SM	Sire Model
3	Estimates, values	BW	Breeding Worth
		c	environmental correlation between records within sub-classes
		EBV	Estimated Breeding Value
		ETA	Estimated Transmitting Ability
		EPD	Expected Progeny Difference
		ME	mature Equivalent, records are adjusted to mature cow yield basis
		PD	Predicted Difference
		PTA	Predicted Transmitting Ability
		RBV	Relative Breeding Value
		REL	Reliability/Repeatability of a sire proof, given either in the scale between 0 and 1 or as percenta
		SD	Standard Deviation
		SE	Standard Error
		TMI	Total Merit Index
		VAR	Variance
4	Population parameters	rg	Genetic correlation
		rp	Phenotypic correlation
		h2	Heritability of a trait
		t	Repeatability of trait
5	Traits of Interest	acw	Adjusted carcass weight
		aww	Adjusted weaning weight
		cae	Calving Ease
		stb	Stillbirth
		bwt	Birth Weight
		pli	Productive Life
		AFC	Age first service
		CAI	Calving interval
		NCA	Number of calvings
6	Type of effect	X	Covariable (expressed as a numerical variable in a continuous scale)
		F	Fixed effect (class variable)
		R	Random effect
		C	Descriptive variable relative to the calf (alving traits), not to be included in the model
7	Model definition	CG	Contemporary group, comparison group
		Y	Dependent variable
		HYS	Herd-Year-Season
		HY	Herd-Year
		DAM	Maternal effects
		MPE	Maternal Permanent Environmental Effect
		PEV	Permanent Environmental Effect
8	Environmental effects	AACA	Age at calving
		PEV	Permanent Environmental Effect
		AACA	Age at calving
		AAWG	Age at weighting
		AAEV	Age at evaluation
		ASEX	Sex of the animal
		CSEX	Sex of calf
		BIRW	Birth weight
		CLAS	Classifier
		HERD	Herd (renumbered)
		PARI	Parity
		SEAS	Season
		SLAH	Slaughter house
		TWIN	Twinning
		YEAR	Calendar year
9	Calf descriptive variables	CASI	Sire of the calf
		CSEX	Sex of the calf
		CABI	Calf birthdate
		CAID	Calf ID

6 FILENAMES

All transferred files should be written in ASCII format and use character encoding: UTF-8

Specifically for the pedigree files, organizations will find access in IDEA to two Python scripts, CheckPedigree.py and CheckLinks.py. Aim of these scripts is to assure that pedigree and linking information are correct prior entering the database environment. To run the script type at the prompt:

Python2.6 CheckPedigree.py –m {organization code⁽¹⁾} –f {pedigree file name}

For more information about the CheckPedigree.py and the CheckLinks.py see Appendix I (a and b).

If the scripts detect no errors in the pedigree or link file then a zip file “IB-ORGCODE-yyyymmddThhmmss.zip.” or “IB202-org_code-yyyymmddThhmmss.zip” would be created. The zip file produced by the Python scripts represent the infile for the Interbull database; no other file would be accepted.

For the time being before the database would be ready to accept performance and parameter file the nomenclature for these types of files would be:

COUNTRY.BREED.FILE.TRAIT_TYPE.DATE⁽²⁾

For example, a file from Ireland with performance for Limousine sent on 2010-01-18 would be called: IRL.LIM.F602.AWW_20100118
A parameter file from the same country and breed would be called IRL.LIM.F603.AWW_20100118

⁽¹⁾ For the Org.Code, see Reference section. ⁽²⁾ date yyyymmdd format

REFERENCES

ISO 3166 Country Codes: http://userpage.chemie.fu-berlin.de/diverse/doc/ISO_3166.html
Breed Codes for International Genetic Evaluation of dairy and beef cattle: http://www.interbull.org/index.php?option=com_content&view=article&id=56&Itemid=77

Guideline to Form Beef and Form_Beef: http://www-interbull.slu.se/Interbeef/General_info/framesida-general.htm

InterBeef link on Interbull website: http://www-interbull.slu.se/Beef_Gen_Ev/framesida-beef.htm

README for CheckPedigree.py

Information about the program:

CheckPedigree.py will perform a series of checks on your pedigree data to insure that the data is all right. If no errors are detected then a zip file will be created. The zip file represents your checked pedigree file to upload to the Interbull Centre IDEA database. For technical reason the program rejects files containing more than a million of data.
The checks relate to:
Check the international identification numbers (animal, sire and dam)
Correct three digit country code as in the ISO 3166 standard (no missing countries allowed)
Correct three digit breed code according to the Interbull breed codes
Correct construction of the alpha-numerical part of the ID (registration numbers, right justified, leading blanks as zeros, all types of characters allowed except ; and ~ )
Missing sires and dams shall be coded as UUUUUUUUUUUUUUUUUUU (i.e. with 19 U)
Check the animal's birth date
Has to be reported in the format YYYYMMDD
If you know only the year of birth then enter it as YYYY0000
If you know year and month of birth then enter them as YYYYMM00
Missing birth dates are coded as 00000000 (or blanks or a single 0)
Check that a male (or female) animal will eventually appear only as sire (or dam)
Check for inconsistent duplicate records (different sire, dam or birthdate)
Check that an animal is always younger than its parents and grandparents

Before Running the Program:

Install Python (Python3, minimum 3.6). Please note that Python2 is no longer supported by developers.
Create a working directory/folder
Download the CheckPedigree.py program from https://idea.interbull.org/software and copy it to your new directory
Copy your pedigree file to the working directory

Running the Program:

Ensure there is a working network connection
Use the command: python CheckPedigree.py -m <ORGCODE> -f <filename>
Use your uppercase ORGCODE as shown on the upper right hand side of the IDEA page.Your organization code is reported within brackets beside the "Logged in as" information.
The program checks its internal version with the value stored on the Interbull server. You will have to download the most recent version if there is a mismatch.
If you want to inspect a pedigree file containing more than a million record you can do so by adding a "-t" at the end of the command line. By doing so, your pedigree will be only tested for its correctedness but no output will be created. The command line to use will be therefore: python CheckPedigree.py -m <ORGCODE> -f <filename> -t

After Running the Program:

If no errors are detected, the pedigree file will be written into a zip file called IB-ORGCODE-yyyymmddThhmmss.zip. Upload the zip file to Interbull's data exchange site: https://idea.interbull.org/.
In case of errors, no zip file will be created. Please correct your data and re-run the program until the data successfully pass all required checks.
Specific information about your pedigree data, descriptive statistics and a summary of errors are written to the file CheckPedigreeLog.txt.
All errors are listed in detail in the file called CheckPedigreeErrors.txt. The following table describes the brief error messages more fully:

Error message

Description

Inconsistent duplicates

An animal appears twice with different sire, dam or birth date

Warning duplicates

An animal appears twice but with same sire, dam and birth date

Illegal character errors

The numerical part of the international ID is not valid

Breed-country error

The breed-country combination is not recognized
- see file CheckPedigreeAuth.txt (created by the program)

Sex coding error

The sex code is neither M nor F

Parent sex error

A male animal (or a female) appears in the dam (or sire) column

Birth date errors

Malformed entry for birth date

Ancestor check

Animal appears older than its parents or grandparents
- if a parent's birth date is unknown, grandparents are checked

Pedigree loops

Animal appears further back in its pedigree tree as an ancestor of itself

Too many animals detected

For technical reason the number of pedigree lines that can be submitted in each file has been limited to 1 million. If your file exceeds such limit you need to split its content into two (or more) files and test each of them with the CheckPedigree.py program

Note

Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again inside IDEA to double-check the pedigree file uploaded in the zip file.
If you need assistance, please do not hesitate to contact us at interbull@slu.se .

README for CheckLinks.py

Information about the program:

CheckLinks.py will perform a series of checks in your format 202 link file to ensure that the data is all right. If no errors are detected then a zip file will be created. The zip file represents your checked links file ready to upload to the Interbull Centre IDEA database.
The checks relate to:
Record type: must be 202
Record length: must be 44
International identification numbers (first ID, second ID)
Correct three digit country code as in the ISO 3166 standard
Correct three digit breed code according to the Interbull breed codes
Allowed breed-country combination
- see file CheckLinksAuth.txt (created by the program)
Correct construction of the numerical part of the ID (registration numbers, right justified, leading blanks as zeros)
UUUUUUUUUUUUUUUUUUU (19 U's) is only allowed for the second ID
Sex code of the two IDs (they must be the same and M or F)

Before Running the Program:

Install Python (Python3, minimum 3.6). Please note that Python2 is no longer supported by developers.
Create a working directory/folder
Download the CheckLinks.py program from https://idea.interbull.org/software and copy it to your new directory
Copy your pedigree link file to the working directory

Running the Program:

Ensure there is a working network connection
Use the command: python CheckLinks.py -m <ORGCODE> -f <filename>
Use your uppercase ORGCODE as shown on the upper right hand side of the IDEA page.Your organization code is reported within brackets beside the "Logged in as" information.
The program checks its internal version with the value stored on the Interbull server. You will have to download the most recent version if there is a mismatch.

After Running the Program:

If no errors are detected, the pedigree file will be written into a zip file called IB202-org_code-yyyymmddThhmmss.zip. Upload the zip file to Interbull's data exchange site https://idea.interbull.org/
In case of errors, no zip file will be created. Please correct your data and re-run the program until the data successfully pass all required checks.
A summary of errors is written to the file CheckLinksLog.txt.
All errors are listed in detail in the file called CheckLinksErrors.txt.

Note:

Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again at the Interbull Centre to double-check the link file uploaded in the zip file.
If you need assistance, please do not hesitate to contact us at interbull@slu.se .

Error message	Description
Inconsistent duplicates	An animal appears twice with different sire, dam or birth date
Warning duplicates	An animal appears twice but with same sire, dam and birth date
Illegal character errors	The numerical part of the international ID is not valid
Breed-country error	The breed-country combination is not recognized - see file CheckPedigreeAuth.txt (created by the program)
Sex coding error	The sex code is neither M nor F
Parent sex error	A male animal (or a female) appears in the dam (or sire) column
Birth date errors	Malformed entry for birth date
Ancestor check	Animal appears older than its parents or grandparents - if a parent's birth date is unknown, grandparents are checked
Pedigree loops	Animal appears further back in its pedigree tree as an ancestor of itself
Too many animals detected	For technical reason the number of pedigree lines that can be submitted in each file has been limited to 1 million. If your file exceeds such limit you need to split its content into two (or more) files and test each of them with the CheckPedigree.py program