Diff for "public/GDE_File706" - Interbull Centre Wiki

Differences between revisions 9 and 17 (spanning 8 versions)

File 706

for uploading of genomic data in GenoEx-GDE database.

Download the word version here

706 format

Field Description

Format

Example

Record type ¹

integer 3

706

Breed of animal ⁴

character 3

BSW

Country of first registration of animal ²

character 3

AUS

Sex

character 1

ID number of animal ⁵

alphanumeric 12

000000A12345

Organization sending this information

character

ANAFI

UUID ⁶

alphanumeric 36

assigned automatically by gxprep.py program

Genotyping laboratory ⁷

character

Weatherbys Ireland

Sample ID ⁸

alphanumeric

S1234WI2001

Additional

for future reference

Array identifier ⁹

alphanumeric

54609_a

AB – Genotype for SNP Index 1 ¹¹	integer 1	0
AB – Genotype for SNP Index 2 ¹¹	integer 1	1
AB – Genotype for SNP Index … ¹¹	integer 1	2
AB – Genotype for SNP Index n ^10,11	integer 1	5

Record type is always 706 for this File Format
ISO 3166-1 alpha-3 codes (3 characters, capital letters)
Breed of evaluation (3 characters, capital letters, BSW, GUE, HOL, JER, RDC, SIM)
Breed of animal (3 characters, capital letters)
Alpha-numerical, Interbull standard, always 12 characters long
UUID, one for every uploaded genotype sequence. Additional information about generation of UUID can be found here.
Genotyping laboratory, among the ones listed in the "Laboratories" table available in the GenoEx-GDE System Data page https://genoex.org/display. If the laboratory is not listed in the table, a request should be sent to GenoEx@slu.se
Sample ID. If unknown, use the word Missing as Sample ID
Array identifier, one of the listed in the "SNP Arrays" table ("Code" column) available in the GenoEx-GDE System Data page https://genoex.org/display.
n is equal to the number of SNPs reported in the stem of the Array identifier
coded SNP values written as a continuous string.
Acceptable values depend on the Illumina coded allele values, according to the following:

BB→0
AB→1
AA→2
‘unknown’→5

706 example

706;BSW;ITA;M;000000A12345;ANARB;09c98b1e-6af8-4254-9768-58d7cd1ddafd;Weatherbys Ireland;S1234WI2001;;54609_a;021010…

706 upload

In order to upload genomic data to GenoEx-GDE database, the file in 706 format has to be zipped. Zip format is the only one accepted by GenoEx-GDE database for the upload. Zip file can be created using the support program gxprep.py as described here: https://interbull.org/ib/gde_gxprep_manual(#zip_example) If the User creates the zip file without using the support program gxprep.py, please make sure that the file containing genotypes in 706 format and compressed in the zip archive has name genotypes.csv.

-  ⇤ ← Revision 9 as of 2021-02-16 14:19:24 → 
  Size: 12759
  Editor: SimoneSavoia
  Comment:
+   ← Revision 17 as of 2025-03-27 15:35:05 → ⇥
  Size: 12941
  Editor: Valentina
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
+== File 706 ==
for uploading of genomic data in !GenoEx-GDE database.
-Line 4:
+Line 6:
-== File 706 ==
for the upload of genomic data in !GenoEx-GDE database.
+Download the word version [[attachment:706file.docx|here|&do=get]]
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-||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">Sample ID ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">alphanumeric ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">S1234WI2001 ||
+||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">Sample ID ^8^ ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">alphanumeric ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">S1234WI2001 ||
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-||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">Array identifier ^8^ ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">alphanumeric ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">54609_a ||
+||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">Array identifier ^9^ ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">alphanumeric ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">54609_a ||
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-||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index 1 ^10^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">0 ||
||<width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index 2 ^10^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">1 ||
||<width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index … ^10^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">2 ||
||<width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index n ^9,10^ ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">5 ||
+||<tablewidth="570px"width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index 1 ^11^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">0 ||
||<width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index 2 ^11^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">1 ||
||<width="259px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index … ^11^ ||<width="131px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:none;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0mm;padding-left:0mm;padding-right:0.49mm">2 ||
||<width="259px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">AB – Genotype for SNP Index n ^10,11^ ||<width="131px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">integer 1 ||<width="167px" style="border-top:none;border-bottom:1.00pt solid #000000;border-left:none;border-right:1.00pt solid #000000;padding-top:0mm;padding-bottom:0.49mm;padding-left:0mm;padding-right:0.49mm">5 ||
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-. UUID, one for every uploaded genotype sequence. Additional information about generation of UUID can be found at https://wiki.interbull.org/public/uuid?action=print
+. UUID, one for every uploaded genotype sequence. Additional information about generation of UUID can be found [[https://interbull.org/ib/uuid_instructions_gde|here]].
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+. Sample ID. If unknown, use the word ''Missing'' as Sample ID
-Line 68:
+Line 69:
-Line 74:
+Line 73:
-Line 76:
+Line 74:
-In order to upload genomic data to !GenoEx-GDE database, the file in 706 format has to be zipped. Zip format is the only one accepted by !GenoEx-GDE database for the upload. Zip file can be created using the support program gxprep.py as described here: https://wiki.interbull.org/public/GDE_gxprep_manual#zip_example
If the User creates the zip file without using the support program gxprep.py, please make sure that the file containing genotypes in 706 format and compressed in the zip archive has name '''genotypes.csv'''.
+In order to upload genomic data to !GenoEx-GDE database, the file in 706 format has to be zipped. Zip format is the only one accepted by !GenoEx-GDE database for the upload. Zip file can be created using the support program gxprep.py as described here: [[https://interbull.org/ib/gde_gxprep_manual#zip_example|https://interbull.org/ib/gde_gxprep_manual]](#zip_example) If the User creates the zip file without using the support program gxprep.py, please make sure that the file containing genotypes in 706 format and compressed in the zip archive has name '''genotypes.csv'''.