Bull Controlling Country list (File 734)

Purpose

Defining which country controls a given AI bull that is used in multiple countries has always been a challenge for Interbull service users, given that country of registration only implies the origin of the animal, not where it actually is located. For progeny tested bulls included in MACE, the country with the larger number of daughters included in the national genetic evaluation usually is a reliable indicator of the controlling country, but this additional information is not available for the young genomically evaluated bulls that are included in GMACE.
Therefore, the Interbull SC has decided to request additional information from the service users regarding which bulls are controlled by companies/stud within the area of influence of each country participating in Interbull international comparisons (MACE & GMACE). This information will have strategic use for interpreting all types of results distributed by Interbull and it will play an important role on the GMACE publication policy.

Implementation

All service users are encouraged to send the bull controlling information to the Interbull Centre using the file 734 format described herein.
1. Each national genetic evaluation centre (NGEC) should include in the file 734 all bulls that are controlled by an AI company, bull stud or individual owner within its area of coverage, usually the country it represents.
2. Both progeny tested and young bulls should be included in file 734.
The files 734 received will be merged and made available to all service users
1. The Interbull Centre will try to resolve all potential conflicts (e.g. same bull declared by different controllers) before distribution by contacting the involved NGECs.

April 2014 run

Those NGECs willing to provide bull controlling information as input to the 2014 GMACE run must provide the file 734 to the Interbull Centre until Feb 28, 2014.
For bulls included in the supplied controlling country list, the GMACE publication status declared by the controlling country will take preference regardless of publication status in other countries.
The previously distributed ”ownership” list will be renamed as ”publication status" list and will contain a list of bulls which comply with the following criteria for the controlling country:
1. Status of bull = 10 (AI bull)
2. Publication status = Y (bull meets the national standards for official publication)
For any bull not included in any user-supplied controlling country file, the bull will be considered publishable in routine/implementation runs if at least one GEBV record included in GMACE, for any population and any trait, has
1. Status of bull = 10 (AI bull)
2. Publication status = Y (bull meets the national standards for official publication)

Future use of file 734

During the 2014 ICAR/Interbull Conference in Berlin, from May 20-21, 2014, the Interbull Centre will present in more detail how the bull controlling country information will be incorporated into the normal data flow. Likewise, the SC will establish in more details how this control information will be used by Interbull and service users.

File 734 format

This format is designed for uploading information about bull controlling country and its GMACE publication status. Note that the file has semi-colon field separators (exactly four) and the column positions allow for these separators.

Column Field description                                   Format        Notes
1      Record type                                         Character  3  734
5      Breed of evaluation                                 Character  3  Notes 1 and 3.
9      Controlling country (Population code)               Character  3  Notes 2 and 3.
13     International animal ID                             Character 19  Note 4.
33     GMACE publication status                            Character  1  Note 5.

Notes:

Breed of evaluation (upper case) must be BSW, GUE, JER, HOL, RDC or SIM.
The population code must be an upper case population code assigned by the Interbull Centre. It is generally the same as the country code of the organization submitting the data except in the cases of multi-country evaluations (eg. "DEA" and "DFS") or multiple populations within a country participating in the same international evaluation (eg. "CHE"/"CHR", "FRA"/"FRR"/"FRM").
The breed-population combination must be among the combinations for which your organization is authorized to submit bull evaluations for MACE for dairy production traits.
The 19-character international animal ID must be valid according to the rules specified for pedigree files (breed*3, country*3, sex*1, id*12). (The animal must exist in the Interbull pedigree database and a pedigree record must have been uploaded.)
The allowed "GMACE publication status codes" are: Y=yes, the controlling country allows the GMACE results for that bull to be distributed, N=no, the controlling country DOES NOT allow the GMACE results for that bull to be distributed or P=progeny tested bull (i.e. not included in GMACE).

Sample records:

734;HOL;ITA;HOLITAM000123456789;Y
734;HOL;ITA;HOLITAM000987654321;N
734;HOL;ITA;HOLITAM000987654322;N
734;HOL;ITA;HOLAUTM012345678900;Y
734;HOL;ITA;HOLITAM000987654323;Y

-  ⇤ ← Revision 1 as of 2014-02-17 11:12:19 → 
  Size: 6163
  Editor: João
  Comment:
+   ← Revision 8 as of 2014-02-17 14:08:26 → ⇥
  Size: 5535
  Editor: João
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+{{attachment:interbull loggo webb.png}}
-Line 4:
+Line 6:
-Defining which country controls a given AI bull that is used in multiple countries has always been a challenge for Interbull service users, given that country of registration only implies the origin of the animal, not where it actually is located. For progeny tested bulls included in MACE, the country with the larger number of daughters included in the national genetic evaluation usually is a reliable indicator of the controlling country, but this additional information is not available for the young genomically evaluated bulls that are included in GMACE.
+Defining which country controls a given AI bull that is used in multiple countries has always been a challenge for Interbull service users, given that country of registration only implies the origin of the animal, not where it actually is located. For progeny tested bulls included in MACE, the country with the larger number of daughters included in the national genetic evaluation usually is a reliable indicator of the controlling country, but this additional information is not available for the young genomically evaluated bulls that are included in GMACE. <<BR>>
-Line 9:
+Line 11:
-. All countries sending data for GMACE have the option to send a list of bulls which they claim to have the control over until Feb 28, 2014. 
 1. The lists received will be merged and made available to all participating countries, shortly after data reception, allowing potential conflicts to be resolved before distribution. 
 1. For bulls included in the supplied controlling country list, publication status declared by the controlling country will take preference regardless of publication status in other countries. 
 1. The previously distributed ”ownership” list will be renamed as ”publication status" list and will contain a list of bulls which comply with the following criteria for the controlling country:
+. All service users are encouraged to send the bull controlling information to the Interbull Centre using the file 734 format described herein.
  a. Each national genetic evaluation centre (NGEC) should include in the file 734 '''all bulls that are controlled by an AI company, bull stud or individual owner within its area of coverage''', usually the country it represents.
  a. '''Both progeny tested and young bulls''' should be included in file 734.
 1. The files 734 received will be merged and made available to all service users
  a. The Interbull Centre will try to resolve all potential conflicts (e.g. same bull declared by different controllers) before distribution by contacting the involved NGECs. 

== April 2014 run ==
 1. Those NGECs willing to provide bull controlling information as input to the 2014 GMACE run must provide the file 734 to the Interbull Centre until '''Feb 28, 2014'''. 
 1. For bulls included in the supplied controlling country list, the GMACE publication status declared by the controlling country will take preference regardless of publication status in other countries. 
 1. The previously distributed ”ownership” list will be renamed as ”publication status" list and will contain a list of bulls which comply with the following criteria '''for the controlling country''':
-Line 15:
+Line 23:
-. For any bull not included in any user-supplied controlling country file, the bull will be considered publishable in routine runs if at least one GEBV record included in GMACE, for any population and any trait, has
+. For any bull not included in any user-supplied controlling country file, the bull will be considered publishable in routine/implementation runs if at least one GEBV record included in GMACE, for any population and any trait, has
-Line 18:
+Line 26:
-. Given that the Feb 2014 GMACE test run determines which changes can be implemented in both the April and August runs the publication policy adopted by participating countries must reflect the national policy to be adopted in both following runs.
-Line 20:
+Line 27:
-This format is designed for uploading information about which animals have been genotyped, usually using whole genome SNP chips. Note that the file has semi-colon field separators (exactly eight) and the column positions allow for these separators.
+== Future use of file 734 ==
During the 2014 ICAR/Interbull Conference in Berlin, from May 20-21, 2014, the Interbull Centre will present in more detail how the bull controlling country information will be incorporated into the normal data flow. Likewise, the SC will establish in more details how this control information will be used by Interbull and service users.

== File 734 format ==
This format is designed for uploading information about bull controlling country and its GMACE publication status. Note that the file has semi-colon field separators (exactly four) and the column positions allow for these separators.
-Line 23:
+Line 34:
-Column Field description                                   Format       Notes
1      Record type                                         Character 3  733
5      Breed of evaluation                                 Character 3  Notes 1 and 3.
9      Population of evaluation                            Character 3  Notes 2 and 3.
13     International animal ID                             Character19  Note 4.
33     Genotyping chip code                                Character10  Note 5.
44     Genotype status code (U/P/A/G/T/)                   Character 1  Note 6.
46     Share code (right to share genotype (Y/N))          Character 1  Note 7.
48     Tissue code (Availability of tissue for genotyping) Character 1  Note 8.
50     Publish code (right to publish thi info (Y/N)       Character 1  Note 9.
+Column Field description                                   Format        Notes
1      Record type                                         Character  3  734
5      Breed of evaluation                                 Character  3  Notes 1 and 3.
9      Controlling country (Population code)               Character  3  Notes 2 and 3.
13     International animal ID                             Character 19  Note 4.
33     GMACE publication status                            Character  1  Note 5.
-Line 34:
+Line 41:
-Notes:
-Line 36:
+Line 42:
-. Breed of evaluation must be one of BSW, GUE, JER, HOL, RDC or SIM if the animal is submitted for Interbull evaluations or UUU otherwise.
 1. The population code must be an upper case population code assigned by the Interbull Centre. It is generally the same as the country code of the organization submitting the data except in the cases of multi-country evaluations (eg. "DEA" and "DFS") or multiple populations within a country participating in the same international evaluation (eg. "CHE"/"CHR", "FRA"/"FRR"/"FRM"). <<span(style="background-color: #FFFF00;")>>If the animal will not be submitted to Interbull evaluations use code "UUU".<<span>> <<span(style="color: #000080;")>>i.e., not submitted for MACE<<span>>
 1. The breed-population combination must be among the combinations for which your organization is authorized to submit bull evaluations for MACE for dairy production traits, or "UUU;UUU" for animals which will not be submitted to Interbull evaluations.
+'''''Notes:'''''
''
 1. Breed of evaluation (upper case) must be BSW, GUE, JER, HOL, RDC or SIM.
 1. The population code must be an upper case population code assigned by the Interbull Centre. It is generally the same as the country code of the organization submitting the data except in the cases of multi-country evaluations (eg. "DEA" and "DFS") or multiple populations within a country participating in the same international evaluation (eg. "CHE"/"CHR", "FRA"/"FRR"/"FRM").
 1. The breed-population combination must be among the combinations for which your organization is authorized to submit bull evaluations for MACE for dairy production traits.
-Line 40:
+Line 48:
-. The "chip" code must be among the foreseen list present in the DB (eg., None, Parentage, Illu3K, IlluLD, Illu50K, Illu50K2, CRV60K, CRV60K2, IlluHD, AffyHD, Sequence, GGP9K, Unknown)
 1. The allowed "status codes" are: U=unavailable, P=genotyping in progress A=available but not yet used for GEBVs, G=used for GEBVs but not yet used in training, T=used for training for protein yield.
 1. The allowed "share codes" are: Y=yes, the country submitting the data is considering sharing or N=no, the country submitting the data is not considering sharing
 1. The foreseen "tissue codes" are: N=none, B=blood, S=semen, H=hair bulbs, E=ear punch, M=multiple or U=unknown. This field is available to signal access to biological material on animals which may be of interest to others.
 1. The allowed "publish codes" are: Y=yes or No. This field indicates whether the information in this specific record may be made available to other organizations (Y) or only to the Interbull Centre (N).
+. The allowed "GMACE publication status codes" are: Y=yes, the controlling country allows the GMACE results for that bull to be distributed, N=no, the controlling country DOES NOT allow the GMACE results for that bull to be distributed or P=progeny tested bull (i.e. not included in GMACE).
''
-Line 46:
+Line 51:
-'''Sample records:'''
+=== Sample records: ===
-Line 49:
+Line 54:
-;BSW;ITA;BSWAUTM012345678900;Illu50K   ;G;Y;U;Y
733;BSW;ITA;BSWITAM000123456789;IlluLD    ;T;Y;U;Y
733;BSW;ITA;BSWITAM000987654321;Illu50K2  ;G;Y;U;Y
733;BSW;ITA;BSWITAM000987654322;None      ;U;N;B;Y
733;BSW;ITA;BSWITAM000987654323;Sequence  ;P;Y;S;Y
+;HOL;ITA;HOLITAM000123456789;Y
734;HOL;ITA;HOLITAM000987654321;N
734;HOL;ITA;HOLITAM000987654322;N
734;HOL;ITA;HOLAUTM012345678900;Y
734;HOL;ITA;HOLITAM000987654323;Y