Schema information

Table of Contents

  1. Schema quick view
  2. International schema information
  3. Selection lists
    1. English
      1. FILE_TYPE entry codes
      2. PROJECT entry codes
      3. TRANSACTION_TYPE entry codes
  4. Language-independent schema details
  5. Language-specific schema details
    1. English
  6. Schema SAIDs

Name: Genotype File Layout
Description: Data schema for the pedigree file layout for the Net-Zero Dairy Genome Project
Classification: RDF402
Author: Ricarda E. Jahnel
Author Email: rjahnel@uoguelph.ca
ICT Group: NDGP

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Schema quick view

Attribute Label Description
ANIMAL_ID ANIMAL_ID INTERBULL REGISTRATION CODE WHICH HAS EXACTLY 19 CHARACTERS. MADE UP OF FOUR COMPONENTS: BREED (3), COUNTRY (3), SEX(1), REGISTRATION NUMBER(12)
DATE_OF_GENOTYPE_TEST DATE_OF_GENOTYPE_TEST  
FILE_TYPE FILE_TYPE  
GENOTYPE GENOTYPE USING THE CDCB FORMAT ; THE GENOTYPE IS A VARIABLE LENGTH STRING OF 0,1,2,5 INDICATING SNP GENOTYPES OF BB, AB, AA, – (1 BYTE PER SNP, NO COMMAS BETWEEN SNPS). FOR EXAMPLE ‘01252010250211110025…….’.
IMPUTATION_USED_TO_GENERATE_DATA IMPUTATION_USED_TO_GENERATE_DATA YES or NO
PANEL_TYPE_BEFORE_IMPUTATION PANEL_TYPE_BEFORE_IMPUTATION  
PROJECT PROJECT  
SAMPLE_ID SAMPLE_ID UNIQUELY IDENTIFIES GENOTYPE (ie. SENTRIX CODE); DO NOT USE THE ANIMAL_ID (REGISTRATION NUM) TO ALLOW FOR MULTIPLE GENOTYPES PER ANIMAL IF REQUIRED
SNP_CHIP_PANEL_TYPE SNP_CHIP_PANEL_TYPE  
SOURCE_OF_DATA SOURCE_OF_DATA See contacts list under ‘Source of Data’ column
TRANSACTION_TYPE TRANSACTION_TYPE  

International schema information

Language Name Description
English Genotype File Layout Data schema for the pedigree file layout for the Net-Zero Dairy Genome Project

Selection lists

English

FILE_TYPE entry codes

Entry code Label
01 Pedigree
02 Calving
03 Production
04 Events
05 Genotype
06 Milk data

PROJECT entry codes

Entry code Label
100 EDGP
101 EDGP & NAEX
102 NDGP
110 EDGP & RDGP
111 EDGP & RDGP & NAEX
001 NAEX
010 RDGP
011 RDGP & NAEX

TRANSACTION_TYPE entry codes

Entry code Label
D Delete
U Update

Language-independent schema details

Attribute Sensitive Unit Type Character encoding Required entry
ANIMAL_ID false   Text utf-8 true
DATE_OF_GENOTYPE_TEST false   DateTime utf-8 true
FILE_TYPE false   Text utf-8 true
GENOTYPE false   Text utf-8 true
IMPUTATION_USED_TO_GENERATE_DATA false   Text utf-8 true
PANEL_TYPE_BEFORE_IMPUTATION false   Text utf-8 false
PROJECT false   Text utf-8 true
SAMPLE_ID false   Text utf-8 true
SNP_CHIP_PANEL_TYPE false   Text utf-8 true
SOURCE_OF_DATA false   Text utf-8 true
TRANSACTION_TYPE false   Text utf-8 true

Language-specific schema details

English

Attribute Label Description List
ANIMAL_ID ANIMAL_ID INTERBULL REGISTRATION CODE WHICH HAS EXACTLY 19 CHARACTERS. MADE UP OF FOUR COMPONENTS: BREED (3), COUNTRY (3), SEX(1), REGISTRATION NUMBER(12) Not a list
DATE_OF_GENOTYPE_TEST DATE_OF_GENOTYPE_TEST   Not a list
FILE_TYPE FILE_TYPE   Pedigree, Calving, Production, Events, Genotype, Milk data
GENOTYPE GENOTYPE USING THE CDCB FORMAT ; THE GENOTYPE IS A VARIABLE LENGTH STRING OF 0,1,2,5 INDICATING SNP GENOTYPES OF BB, AB, AA, – (1 BYTE PER SNP, NO COMMAS BETWEEN SNPS). FOR EXAMPLE ‘01252010250211110025…….’. Not a list
IMPUTATION_USED_TO_GENERATE_DATA IMPUTATION_USED_TO_GENERATE_DATA YES or NO Not a list
PANEL_TYPE_BEFORE_IMPUTATION PANEL_TYPE_BEFORE_IMPUTATION   Not a list
PROJECT PROJECT   EDGP, EDGP & NAEX, NDGP, EDGP & RDGP, EDGP & RDGP & NAEX, NAEX, RDGP, RDGP & NAEX
SAMPLE_ID SAMPLE_ID UNIQUELY IDENTIFIES GENOTYPE (ie. SENTRIX CODE); DO NOT USE THE ANIMAL_ID (REGISTRATION NUM) TO ALLOW FOR MULTIPLE GENOTYPES PER ANIMAL IF REQUIRED Not a list
SNP_CHIP_PANEL_TYPE SNP_CHIP_PANEL_TYPE   Not a list
SOURCE_OF_DATA SOURCE_OF_DATA See contacts list under ‘Source of Data’ column Not a list
TRANSACTION_TYPE TRANSACTION_TYPE   Delete, Update

Schema SAIDs

Capture base: EOL30trcT6Ce7zyxj2QfV5JOVKH5sfXVXOJdsBhoh6vI

Layer SAID
character_encoding ERpREYa0K5_cCUKhpTdjqnFRcrT7YW3VvQ1OjZyOgSpE
conformance EiEoX0KsQqLEuqu0RXb3dJMYdkE8eYXmOw6NDY9X9J7U
entry (en) EezMLqk4brFrEQ2GSXm6YxzAqoF11aNwrxTt5j2zqy00
entry_code EN7JzZkAFgfPCPL4XMISP_a4Yro2XXZCLzGiivnRw1BY
information (en) Ersu-KzbK_Bi8yCxhjTB_4UXXpdFRsCFf-OtLs7HokLw
label (en) EVRBJKKLTrgOgoLDN0iKz24klj6Ao_SHZsF9M4pvUbgY
meta (en) EbXS1-PaSbc4whUAdnBr3Ct442ELMrxtSyhiZQuyabA0

Date created: 2025-04-29 13:50:02