Guidelines to Join Interbeef International Genetic Evaluations
Contents
1. Guidelines to Join Interbeef International Genetic Evaluations Version 2 3 InterBeef 24 October 2012 Contact Interbull Centre Dept Animal Breeding and Genetics 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 Table of Contents 1 INTRODUCTION bi vsssssssssisecss sossssisvscssessseassosenssasnsecssssscanessnsacvaseessobaeesssososesssuaseesssoaseedesecsoessseassess 4 2 THE ANIMAL INTERNATIONAL IDENTIFICATION 0 u sccccssssscssssssccssssccccssscccessssccessnee 4 2 1 FORMAT 4 20 CONSTRUCTING THE INTERNATIONAL IDENTIFICATION 4 2 3 THE NEW WEB INTERFACE AT 5 3 THE REQUIRED FILES siisesscisssasecctessetessdsacsssssetacssesacsscvestevsssdsconssacsedesedess sassaceasbesassacessessesecsdesses 6 3 1 THE DIFFERENT INTERBEEF 5 6 3 2 GENERAL PRINCIPLES FOR FILE PREPARATION ccccesececececseecsesescsceescececececscecseseeceeseseseseeeeeecs 6 3 3 THE NATIONAL PEDIGREE FILE 601 7 3 4 THE PERFORMANCE FILE 602 sse cccssssccessssecesssnsecessoseesesssecsensssessenessesssnsecsesnsecssessessensess 8 3 5 P2. 93 10 XII 2 Variable total file length depending on the number of environmental effects included in the model Ex ENV 1 length 102 ENV 2 length 113 ENV 3 length 124 etc Repeat this field times 1 NENV adding one 1 empty space between fields Notes l See trait codes in Table 4 abbreviations See Reference section for Breed codes See Reference section for Country codes ISO 3166 Alpha 3 IV Sex Male F Female only Vv Identification Number in Interbull Format Alpha numeric codes only Right justified Left blanks being filled with T single birth 2 twin birth Vil 0 noET 1 ET Vill 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 Identification of the contemporary group Xl 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 trait breed combin
3. Animal s SIRE Breed of the sire SBREED Char 25 O LIM Country of birth SIIDC Char 28 O FRA Sex SSEX Char 31 110 M ID code of the sire SIID Char 32 120 IV 95015085 International ID of Animal s DAM Breed of the dam DBREED Char 45 O LIM Country of birth DIIDC Char 48 O FRA Sex DSEX Char 51 110 IlI F ID code of the dam DIID Char 52 1210 IV 1111001111 Additional information Date of birth of animal BDATE Int 65 810 V 20010130 Name of animal NAME Char 74 3010 Faust Country sending information RCOU Char 105 3 M FRA Status amp Mandatory Optional Note See Reference section for Breed codes ll See Reference Section for Country codes ISO 3166 Alpha 3 Sex Male amp Female only IV Identification Number in Interbull Format Right justified Leading blanks filled with Zero 0 Vv 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 ab
4. CheckLinks py m lt ORGCODES f lt filename gt e Use your uppercase ORGCODE as shown the upper right hand side of the IDEA page Your organization code is reported within brackets beside the Logged in as information e 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 14 A summary of errors is written to the 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
5. authoritative organization Therefore whenever you submit pedigree data the system first checks that the combination country breed 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 CHAFRAM8 65412398745 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
6. then countries will proceed sending performance file file 602 and parameter file file 603 to the Interbull ftp server 3 2 General principles for file preparation e Numeric information must be right justified e Characters must be left justified All characters should be in upper case 3 3 national pedigree 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 Status Note Example Record type RTYPE Char 1 3 601 International ID of ANIMAL Breed of the animal ABREED Char 5 M LIM Country of birth AIDC Char 8 M Il FRA Sex ASEX Char 11 1 Ill F ID code of the animal AID Char 12 12 M IV 8795005065 International ID of
7. 10 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 htm Breed Codes for International Genetic Evaluation of dairy and beef cattle http www interbull org index php option com_content amp view article amp id 56 amp ltemid 77 Guideline to Form Beef and Form 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 APPENDIX CheckPedigree py Information about 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 The checks relate to e Check the international identification numbers animal sire and dam o 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 numerical part of the ID registration numbers right justified leading blanks as zeros o Missing sires and dams shall be coded as UUUUU
8. ARAMETER 603 E aie oid nities 9 3 6 ABBREVIATIONS ccsscsceeesecececececececscececeeseseseseeeseseseeeeeseseseseecseeceeseseseecececsesceeeeecececececeeececececess 10 4 1 REFERENCES ssvcdesscastelssssoudatssevessesdecedcessesvsbasscestadcudsestescedeseessesvasedsentessisbussesseccceeass 11 APPENDIX I A CHECKPEDIGREE PY cccssssscssssssccssssccccssscccssssccccssssccscssseccscssccccssaccecesssees 12 5 APPENDIX CHECKLINKS PY cscscssssssssrsesssssrsersessrsnssssssessessssesscssnsessesensessessnenseeses 14 1 INTRODUCTION Countries willing to join InterBeef must be members of Interbull and support the ICAR guidelines for data collection http Avww 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 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 refers to the breed of identification of the animal in its country of first registration in most cases the country of origin 3 cha
9. EV 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 10 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 f pedigree file name For more information about the CheckPedigree py and the CheckLinks py see Appendix 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 For example a file from Ireland with performance for Limousine sent on 20
10. T Embryo Transfer Kg Kilogram MGS Maternal Grand Sire NS Natural Service Ib Pounds 2 Genetic evaluation AM Animal Model methods 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 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 percentage SD Standard Deviation SE Standard Error TMI Total Merit Index VAR Variance 4 Population parameters 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 Sitillbirth 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 P
11. UUUUUUUUUUUUUU i e with 19 U e 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 YY Y Y0000 If you know year and month of birth then enter them as o Missing birth dates are coded as 00000000 or blanks or a single 0 e Check that a male or female animal will eventually appear only as sire or dam e Check for inconsistent duplicate records different sire dam or birthdate e Check that an animal is always younger than its parents and grandparents Before Running the Program 1 Install Python version 2 5 to 2 7 if necessary 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 e Ensure there is a working network connection e Use the command python CheckPedigree py m lt ORGCODES f lt filename gt e 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 e 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 IB ORGCODE
12. ation all fields are mandatory Field description Label Format Starting Field Note Example byte Length Record type RTYPE Char 1 3 603 Trait FCODE Char 5 3 1 AWW Breed of evaluation EBREED Char 9 3 Il LIM Country sending information RCOU Char 13 3 Ill FRA Reference age or class REF Int 17 5 IV 200 Trait heritability H2 Int 23 25 Contemporary group CG Char 27 20 VI HYS How GG is fitted in the model type of effect CGT Char 48 1 VII R Maternal genetic effect fitted in the model DAM Char 50 1 VIN N Maternal permanent environmental effect fitted MPE Char 52 1 VIII N in the model Permanent environmental effect fitted in the PEV Char 54 1 VII Y Number of environmental effects included in the NENV Int 56 3 IX 4 national model Environmental effect ENV n Char 60 20 X SEAS How ENV n is fitted in the model type of ENVT n Char 81 1 VII F Variable total file length depending on the number of environmental effects included in the model ENV 1 length 81 ENV 2 length 105 ENV 3 length 128 etc Repeat these fields times 1 NENV adding one 1 empty space between fields Notes Ml IV Vv VI vil Vill Use the trait codes in Table 4 abbreviations See Reference section for Breed codes See Reference section for Country codes ISO 3166 Alpha 3 Reference value age or class used to adj
13. files There are 4 groups of files to be created by a country willing to join the international beef genetic evaluation e The 601 file representing the national pedigree file e The 602 file representing the national performance file limited until now to adjusted weaning weights adjusted carcass weight and calving ease e The 603 file representing the parameter file e 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 e 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 e 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 e Once this step has been fulfilled
14. netic 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 The national pedigree file must be first checked with the CheckPedigree py script provided by Interbull 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
15. ove must be recorded Each herd is identified with 15 digits identification coded as characters e The first three digits correspond to the country using the ISO 3166 Alpha 3 system see Reference section e 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 Table 2 602 file format all fields are mandatory Field description Label Format Starting byte Field Note Example Record type RTYPE Char 1 3 602 Trait FCODE Char 5 3 jl AWW Breed of evaluation EBREED Char 9 3 Il LIM Country sending information RCOU Char 13 3 Ill FRA International ID of ANIMAL Breed of the animal ABREED Char 17 3 Il LIM Country of birth AIDC Char 20 3 Ill FRA Sex ASEX Char 23 1 IV 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 HERID Char 41 15 FRA000123456789 Dependent variable Y Char 57 10 IX 245 Contemporary group CG Char 68 20 X 333 Number of environmental effects NENV Int 89 3 Xl 4 included in the national model Environmental effect ENV n Char
16. racters as defined in the Interbull Breed Codes available at www interbull org see Reference section field Country of the 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 male female field Identification number of the 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 e A Charolais CHA e First registered in France FRA male M With the following identification in 006327826864 France Ex 125693456875 refers to Blonde d Aquitaine First registered in Ireland IRL e A female With the following identification in 125693456875 Ireland 2 2 Constructing the international identification number 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 Al straw or embryo is sold abroad the importing co
17. ree file uploaded in the zip file If you need assistance please do not hesitate to contact us at interbull slu se 5 APPENDIX I b 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 e Record type must be 202 e Record length must be 44 e International identification numbers first ID second ID o Correct three digit country code as in the ISO 3166 standard o Correct three digit breed code according to the Interbull breed codes o Allowed breed country combination see file CheckLinksAuth txt created by the program o 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 e Sex code of the two IDs they must be the same and M or F Before Running the Program 1 Install Python version 2 5 to 2 7 if necessary 2 Create a working directory folder 3 Download the CheckLinks py program from https idea interbull org software and copy it to your new directory 4 Copy your pedigree link file to the working directory Running the Program e Ensure there is a working network connection e Use the command python
18. untry 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 LIMIRLF231 112150014 The animal 84106449 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 708376849 and VLR France constructs its AIID as followed CHAFRAM000384 106449 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 Data Exchange Area that allows register users to all the pedigree handling functionalities IDEA is available at httos 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 ge
19. ust the dependent variable Ex reference national weaning age 200 days Trait heritability used in the national evaluation expressed in a scale from 1 100 Description of the contemporary group used The most common are herd year season HYS and herd year HY In case a different definition is adopted describe it briefly 20 characters 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 Declare if this specific effect DAM MPE or PEV is fitted into the national model Y yes Defines the remaining number of fields in the record Additional fields 2 NENV Describes the environmental effect Use the environmental effect codes in Table 4 abbreviations In case trait is not yet included on Table 4 describe it briefly 20 characters e In case of polynomial effects use the effect code followed by the order Ex SEAS should be coded SEAS2 Incase of interactions combine the effect codes in the same field Ex AAWG ASEX should be coded as 3 6 Abbreviations Table 4 List of abbreviations used in Interbull files and documentation Type Abbreviation Meaning 1 General concepts Al Artificial Insemination E
20. yyyymmddThhmmss zip Upload the zip file to Interbull s data exchange site https idea interbull org 12 In case of errors zip file will be created Please correct your data and re run 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 animal appears twice but with same sire dam and birth date Illegal character errors The numerical part of the international ID is not valid The breed country combination is not recognized Pee Oe 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 Animal appears older than its parents or grandparents Ancestor check 7 if a parent s birth date is unknown grandparents are checked 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 pedig
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