Diff for "public/PSE_file_formats" - Interbull Centre Wiki

Differences between revisions 1 and 5 (spanning 4 versions)

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	Numeric	Code of 3 CAPITAL letters according to ISO Country Codes - SENDING COUNTRY
Animal ID - Breed Code	Alphabetic	Code of 3 CAPITAL letters according to ICAR Breed Codes
Animal ID - Nation Code	Numeric	Code of 3 CAPITAL letters according to ISO Country Codes - (part of Interbull animals ID)
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 used to create the SNP record for GenoEx-PSE	Any valid number correctly corresponding to Platform, according to Platform List
Genotype Call Rate	Percent call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE	Percent 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
		.
* Parentage Verification SNP list can be found here

-  ⇤ ← Revision 1 as of 2019-02-07 09:57:41 → 
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+   ← Revision 5 as of 2019-03-22 16:33:46 → ⇥
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  Editor: JoannaSendecka
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-||<width="140px" style="border:none;padding:0in">Service                             User ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Any                           organization abbreviation ||
||<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">Any                          country code ||
||<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">Any breed                               code ||
||<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">Any                               country code ||
+||<width="140px" style="border:none;padding:0in">Service                             User ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Any                           [[http://www.interbull.org/ib/organizationcodes|organization abbreviation]], in CAPITAL letters ||
||<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>>''' ||
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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">Any lab                          ISAG code ||
||<width="140px" style="border:none;padding:0in">Sample ID ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Example:                             ''R1234567890'' ||
||<width="140px" style="border:none;padding:0in">Scan Date ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">Any valid                                 date in the format ''yyymmmdd'' ||
||<width="140px" style="border:none;padding:0in">Platform ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Any SNP                               Platform code ||
||<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">Example:                                 ''55647'' ||
||<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">Example:                             ''99.9'' ||
+||<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">Sample ID ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Example:                             ''R12345 (other allowed values are / ( ) _ - )'' ||
||<width="140px" style="border:none;padding:0in">Scan Date ||<width="332px" style="border:none;padding:0in">Numeric ||<width="218px" style="border:none;padding:0in">Any valid                                 date in the format ''yyyymmdd'' ||
||<width="140px" style="border:none;padding:0in">Platform ||<width="332px" style="border:none;padding:0in">Alphanumeric ||<width="218px" style="border:none;padding:0in">Any SNP                               Platform according to [[https://wiki.interbull.org/public/platforms_arrays|Platform List]] ||
||<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. ||
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+'''* new laboratories, platforms and arrays need to be communicated to Interbull by e-mail prior to data submission.'''
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-||<width="165px" style="border:none;padding:0in">Animal ID                           - Breed Code ||<width="253px" style="border:none;padding:0in">Alphabetic ||<width="260px" style="border:none;padding:0in">Any breed                               code ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Nation Code ||<width="253px" style="border:none;padding:0in">Numeric ||<width="260px" style="border:none;padding:0in">Any                               country code ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Sex Code ||<width="253px" style="border:none;padding:0in">Alphabetic ||<width="260px" style="border:none;padding:0in">'''M'''                           or '''F''' ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Registration ||<width="253px" style="border:none;padding:0in">Alphanumeric ||<width="260px" style="border:none;padding:0in">Example:                            ''A1234567890'' ||
||<width="165px" style="border:none;padding:0in">SNP Name ||<width="253px" style="border:none;padding:0in">Alphanumeric ||<width="260px" style="border:none;padding:0in">Any                           SNP name in                             CAPITALS ||
+||<width="165px" style="border:none;padding:0in">Animal ID                           - Breed Code ||<width="253px" style="border:none;padding:0in">Alphabetic ||<width="260px" style="border:none;padding:0in">Any breed                               code, corresponding to the one in meta.csv file ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Nation Code ||<width="253px" style="border:none;padding:0in">Numeric ||<width="260px" style="border:none;padding:0in">Any                               country code, corresponding to the one in meta.csv file ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Sex Code ||<width="253px" style="border:none;padding:0in">Alphabetic ||<width="260px" style="border:none;padding:0in">'''M'''                           or '''F''', corresponding to the one in meta.csv file ||
||<width="165px" style="border:none;padding:0in">Animal ID                           - Registration ||<width="253px" style="border:none;padding:0in">Alphanumeric ||<width="260px" style="border:none;padding:0in">Example:                            ''A1234567890'', corresponding to the value in meta.csv file ||
||<width="165px" style="border:none;padding:0in">SNP Name ||<width="253px" style="border:none;padding:0in">Alphanumeric ||<width="260px" style="border:none;padding:0in">Any                           SNP name in                             CAPITALS* ||
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+||<width="165px" style="border:none;padding:0in"> ||<width="253px" style="border:none;padding:0in"> ||<width="260px" style="border:none;padding:0in">. ||
||||||<width="165px" style="border:none;padding:0in;text-align:center">'''* Parentage Verification SNP list can be found [[https://wiki.interbull.org/public/PV_SNPs|here]]''' ||