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| Deletions are marked like this. | Additions are marked like this. |
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| ||<tablewidth="1069px" tableheight="458px"width="140px" style="border:none;padding:0in">Record Type ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">702 || | ||<tablewidth="1205px" tableheight="496px"width="140px" style="border:none;padding:0in">Record Type ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">702 || |
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| ||<width="140px" style="border:none;padding:0in">Source Country of Animals ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to [[http://kirste.userpage.fu-berlin.de/diverse/doc/ISO_3166.html|ISO Country Codes]] - '''SENDING COUNTRY'''<<BR>> || ||<width="140px" style="border:none;padding:0in">Animal ID - Breed Code ||<width="332px" style="border:none;padding:0in">Alphabetic ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to [[http://www.interbull.org/ib/icarbreedcodes|ICAR Breed Codes]]<<BR>> || ||<width="140px" style="border:none;padding:0in">Animal ID - Nation Code ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to ISO Country Codes - '''(part of Interbull animals ID)<<BR>>''' || |
||<width="140px" style="border:none;padding:0in">Source Country of Animals ||<width="332px" style="border:none;padding:0in">Alphabetic ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to<<BR>> [[http://kirste.userpage.fu-berlin.de/diverse/doc/ISO_3166.html|ISO Country Codes]] - '''SENDING COUNTRY'''<<BR>> || ||<width="140px" style="border:none;padding:0in">Animal ID - Breed Code ||<width="332px" style="border:none;padding:0in">Alphabetic ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to<<BR>> [[http://www.interbull.org/ib/icarbreedcodes|ICAR Breed Codes]]<<BR>> || ||<width="140px" style="border:none;padding:0in">Animal ID - Nation Code ||<width="332px" style="border:none;padding:0in">Alphabetic ||<width="218px" style="border:none;padding:0in">Code of 3 CAPITAL letters according to<<BR>> ISO Country Codes - '''(part of Interbull animals ID)<<BR>>''' || |
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| ||<width="140px" style="border:none;padding:0in">Genotyping Laboratory Identification ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Name and location or genotyping laboratory Example: [[https://wiki.interbull.org/public/PSE_LabList|Weatherbys Ireland *]] || | ||<width="140px" style="border:none;padding:0in">Genotyping Laboratory Identification ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Name and location or genotyping laboratory Example: [[https://interbull.org/ib/pse_laboratories|Weatherbys Ireland]] || |
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| ||<width="140px" style="border:none;padding:0in">No. SNPs in Genotype ||<width="332px" style="border:none;padding:0in">Total number of SNPs in the animal's full genotype used to create the SNP record for GenoEx-PSE ||<width="218px" style="border:none;padding:0in">''Any valid number correctly corresponding to Platform, according to [[https://wiki.interbull.org/public/platforms_arrays|Platform List]]'' || ||<width="140px" style="border:none;padding:0in">Genotype Call Rate ||<width="332px" style="border:none;padding:0in">Percent call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE ||<width="218px" style="border:none;padding:0in">Percent call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE, two decimals. || |
||<width="140px" style="border:none;padding:0in">No. SNPs in Genotype ||<width="332px" style="border:none;padding:0in">Total number of SNPs in the animal's full genotype <<BR>> used to create the SNP record for GenoEx-PSE ||<width="218px" style="border:none;padding:0in">''Any valid number correctly corresponding to Platform, according to [[https://wiki.interbull.org/public/platforms_arrays|Platform List]]'' || ||<width="140px" style="border:none;padding:0in">Genotype Call Rate ||<width="332px" style="border:none;padding:0in">Percent call rate of the animal's full genotype <<BR>> used to create the SNP record for GenoEx-PSE ||<width="218px" style="border:none;padding:0in">Call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE, two decimals. || |
PSE Submission File Formats v1.1
Submissions must uploaded as a ZIP-archive containing two files meta.csv and snps.csv.
Every SNP specific record in snps.csv file must have a corresponding record in meta.csv file and the information regarding country and breed for given individual must be in agreement in both files.
The fields in both files should be comma separated and no blank fields are allowed.
meta.csv
This file contains information related to animals and the genotyping. There must be one line in this file for each animal in the snps.csv.
Field Name |
Description |
Allowed Values |
Record Type |
Numeric |
702 |
Service User |
Alphanumeric |
Any organization abbreviation, in CAPITAL letters |
Source Country of Animals |
Alphabetic |
Code of 3 CAPITAL letters according to |
Animal ID - Breed Code |
Alphabetic |
Code of 3 CAPITAL letters according to |
Animal ID - Nation Code |
Alphabetic |
Code of 3 CAPITAL letters according to |
Animal ID - Sex Code |
Alphabetic |
M or F |
Animal ID - Registration |
Alphanumeric |
Example: A1234567890 |
Genotyping Laboratory Identification |
Alphanumeric |
Name and location or genotyping laboratory Example: Weatherbys Ireland |
Sample ID |
Alphanumeric |
Example: R12345 (other allowed values are / ( ) _ - ) |
Scan Date |
Numeric |
Any valid date in the format yyyymmdd |
Platform |
Alphanumeric |
Any SNP Platform according to Platform List |
No. SNPs in Genotype |
Total number of SNPs in the animal's full genotype |
Any valid number correctly corresponding to Platform, according to Platform List |
Genotype Call Rate |
Percent call rate of the animal's full genotype |
Call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE, two decimals. |
* new laboratories, platforms and arrays need to be communicated to Interbull by e-mail prior to data submission.
snps.csv
This file contains genotype data one or more animals. Four each animal in this file, identified by the four Animal ID fields, there must be a corresponding record in the meta.csv file.
Field Name |
Description |
Allowed Values |
Record Type |
Numeric |
704-AB or 704-TOP |
Animal ID - Breed Code |
Alphabetic |
Any breed code, corresponding to the one in meta.csv file |
Animal ID - Nation Code |
Numeric |
Any country code, corresponding to the one in meta.csv file |
Animal ID - Sex Code |
Alphabetic |
M or F, corresponding to the one in meta.csv file |
Animal ID - Registration |
Alphanumeric |
Example: A1234567890, corresponding to the value in meta.csv file |
SNP Name |
Alphanumeric |
Any SNP name in CAPITALS* |
Allele 1 |
Alphabetic |
A or B for 704-AB; A, C G or Tfor 704-TOP |
Allele 2 |
Alphabetic |
A or B for 704-AB; A, C G or Tfor 704-TOP |
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* Parentage Verification SNP list can be found here |
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