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''Version 2.3 <<BR>>InterBeef <<BR>> 24 October 2012'' ''Version 2.4 <<BR>>!InterBeef <<BR>> 12 December 2012''
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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. 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.
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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.''' <<BR>> 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. 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.''' <<BR>> 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.
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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. 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.
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 * Once this step has been fulfilled then countries will '''proceed''' sending performance file (file 602) and parameter file (file 603) to the Interbull ftp server.  * Once this step has been fulfilled then countries will '''proceed''' sending performance file (file 602), parameter file (file 603) and eventually an ET file (file 604) to the Interbull ftp server.
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=== How to report 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. Calving traits will therefore be reported as maternal traits only. Therefore the ''International ID of ANIMAL'' in the file602 will refer to the '''dam ID'''.

<<BR>>
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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:<<BR>>

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). <<BR>>		 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:<<BR>>

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). <<BR>>
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<<BR>> InterBeef link on Interbull website: http://www-interbull.slu.se/Beef_Gen_Ev/framesida-beef.htm <<BR>> !InterBeef link on Interbull website: http://www-interbull.slu.se/Beef_Gen_Ev/framesida-beef.htm

interbeef_logo.jpg

Guidelines to Join Interbeef

Version 2.4
InterBeef
12 December 2012

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@hgen.slu.se
URL : http://www.icar.org/pages/working_groups/wg_interbeef.htm

Contents

  1. Guidelines to Join Interbeef
    1. 1. INTRODUCTION
    2. 2. The Animal International Identification
    3. 2.1 Format
    4. 2.2 Constructing the international identification number
    5. 2.3 The New Web Interface at Interbull
    6. 3. The required files
    7. 3.1 The Different InterBeef steps
    8. 3.2 General principles for file preparation:
    9. 3.3 The national pedigree file (601 file)
    10. 3.4 The performance file (602)
      1. How to report calving traits
    11. 3.5 Parameter file (603)
    12. 3.6 ET file (604)
    13. 3.7 Abbreviations
    14. 4 Filenames
    15. References
  2. README for CheckPedigree.py
      1. Information about the program:
      2. Before Running the Program:
      3. Running the Program:
      4. After Running the Program:
      5. Note
  3. README for CheckLinks.py
      1. Information about the program:
      2. Before Running the Program:
      3. Running the Program:
      4. After Running the Program:
      5. Note:

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: BAQIRL125693456875 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@hgen.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 4 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 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 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 proceed sending performance file (file 602), parameter file (file 603) and eventually an ET file (file 604) to the Interbull ftp server.

3.2 General principles for file preparation:

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

3.3 The national pedigree file (601 file)

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.

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

Field description

Label

Format

Start

Length

Statusa

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

3.4 The performance file (602)

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.

How to report 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. Calving traits will therefore be reported as maternal traits only. Therefore the International ID of ANIMAL in the file602 will refer to the dam ID.


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

  • Performance file

Field description

Label

Format

Starting byte

Fielda

Note

Example

Record type

RTYPE

Char

1

3

602

Trait

FCODE

Char

5

3

I

AWW

Breed of evaluation

EBREED

Char

9

3

II

LIM

Country sending information

RCOU

Char

13

3

III

FRA

International ID of ANIMAL

Breed of the animal

ABREED

Char

17

3

II

LIM

Country of birth

AIDC

Char

20

3

III

FRA

Sex

ASEX

Char

23

1

IV

F

ID code of the animal

AID

Char

24

12

V

008795005065

Twinning

TWI

Int

37

1

VI

1

Embryo transfer

ET

Int

39

1

VII

0

Herd

HERID

Char

41

15

VIII

FRA000123456789

Dependent variable

Y

Int

57

10

IX

245

Number of environmental effects included in the national model

NENV

Int

68

3

XI

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

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. 245 Kg (no decimals)

XI

Defines the remaining number of fields in the record. Additional fields = NENV

XII

Value of the respective environmental effect for the current record. Ex. season = 2 (out of 4 classes); birth weight = 36 (kg); sex of calf = F

3.5 Parameter file (603)

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.

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

Field description

Label

Format

Starting byte

Field Lengtha

Note

Example

Record type

RTYPE

Char

1

3

603

Trait

FCODE

Char

5

3

I

AWW

Breed of evaluation

EBREED

Char

9

3

II

LIM

Country sending information

RCOU

Char

13

3

III

FRA

Reference age or class

REF

Int

17

5

IV

200

Trait heritability

H2

Int

23

3

V

25

Minimum number of observation per CG

CGN

Int

27

10

5

Twins

TWIN

Char

38

1

VIII

Y

Maternal (genetic) effect fitted in the model

DAM

Char

40

1

VIII

N

Maternal permanent environmental effect fitted in the model

MPE

Char

42

1

VIII

N

Permanent environmental effect fitted in the model

PEV

Char

44

1

VIII

Y

Number of environmental effects included in the national model

NENV

Int

46

3

IX

4

Environmental effect (n)b

ENV(n)

Char

50

20

X

SEAS

How ENV(n) is fitted in the model (type of effect)b

ENVT(n)

Char

71

1

VII

F

  • b Repeat 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)

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 nth 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

3.6 ET file (604)

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.

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

Field description

Label

Format

Start

Length

Statusa

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”)

3.7 Abbreviations

Table 4: 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 Grand Sire

NS

Natural Service

lb

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

Restricted 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

6

Type of effect

X

Covariable (expressed as a numerical variable in a continuous scale)

F

Fixed effect (class variable)

R

Random effect

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

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

4 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:

  1. Install Python (Python3, minimum 3.6). Please note that Python2 is no longer supported by developers.

  2. Create a working directory/folder

  3. Download the CheckPedigree.py program from https://idea.interbull.org/software and copy it to your new directory

  4. 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 .

public/beef_guidelines (last edited 2021-12-14 14:31:56 by SimoneSavoia)