GenoEx- PSE – User's Manual

This document describes the procedures for the upload and download of the data for the GenoEx-PSE service. The PSE Code of Practice you can find here

The User Manual describes in detail the required file formats, login process and usage of the service itself both for data upload and data download.

Please note that GenoEx service is under regular improvement and thus new functionalities may be introduced. It is therefore important to always use the latest version of this manual.

After you have signed the User’s Agreement and joined the service, you will receive login details from Interbull Center for the users you have requested access for. From this moment you are entitled to use the GenoEx-PSE service via genoex.org.

The login tab can be found on the top right corner of the front page. If you have lost or forgotten your password, a new password can be requested from the Lost Password page, which can be accessed both under the login tab and from the login page. Once you log in you can change your password by pressing the Change password under your username tab in the top right corner. We highly recommend that you change the password from the one provided to you, at the very first login.

Under the About tab, you will find links to all documentation relevant for the GenoEx-services.

Under the Contact tab you will find information needed to contact Interbull Center should you have any questions, comments or concerns regarding the platform or the service.

On the System Data page, four tables are presented: SNP Arrays, Laboratories, Breeds, and Countries. All of the tables have clickable headers, and a search field to ease the looking up of information. The information in these tables represent the only allowed values for the information regarding SNP array, genotyping laboratory, breed and country in the files to be uploaded. See the section for file format for more information

The History tab directs you to the history page, where you find a table showing all the uploads or downloads done by any user of your organization. The history table as well as downloads and uploads, found under the PSE-tab, will be described in the following sections.

Data Upload

To access the Upload page, go to the PSE tab and click Upload. The data to be uploaded must be presented in a .zip-file as described in section 1 of the Users Manual. Details of the file format you can find HERE. Click the Browse button, find and select the file to be uploaded, and then click UPLOAD.

After pressing the UPLOAD button, you will be redirected to a status-page showing the job-id, job type, current status and the date and time, as shown in the pictures below.

An uploading process can have four different statuses: Initiated, Processing, Finished or Failed. At the initial re-direction from the upload page, the current status will be shown as Initiated. The duration of the upload process depends on the size of your file. To follow the progress of your upload, you can either refresh the status page as shown in the three following pictures, or go to the History table. When the Processing is complete, and the upload is either successful or failed, you will receive a notificiation via e-mail to the e-mail address connected to your GenoEx user account.

Failed upload

In the case where the upload is unsuccessful, the job status will be displayed as Failed. The number of errors and the cause of the failed upload will be shown. In the case presented in the image below, the upload failed as the animal-ID used in the snps.csv-file did not correspond to the animal-ID used in the meta.csv-file.

Data extraction

To access the download page, go to the PSE-tab and click Download.

In the download page, query the desired data by sex, breed and country. A selection must be done in all three fields for the extraction to be initiated. In order to select more than one criteria use CTRL+click.

The data can be extracted either in TOP-format or in AB-format, independently of the format that it was submitted in.

In cases where animals is represented with more than one genotype, the Best only will give you the genotype with the highest call rate. By selecting All you will be provided with all the genotypes your organization have access to.

Specific time periods of when data has been uploaded can be select, to for example only download data that has become available since your latest download. The dates provided by default gives you all data uploaded to the database that your organization has access to.

When all the extraction criteria are selected, click CREATE EXTRACTION.

After clicking CREATE EXTRACTION, you will be redirected to a status-page showing the job-id, job type, current status and the date and time, as shown in the pictures below.

A downloading process can have two different statuses: Processing or Finished. At the initial re-direction from the upload page, the current status will be shown as Processing. The duration of the download process depends on the amount of data that is extracted. To follow the progress of your download, you can either refresh the status page as shown in the two following pictures, or go to the History table. When the Processing is complete, and the download is Finished, you will receive a notificiation via e-mail to the e-mail address connected to your GenoEx user account.

When the extraction is completed, you can fetch the extracted file by clicking on Download extracted file on the jobs status page. The downloaded file can be fetched either directly, or at a later time and date. The data will be presented in a zipped folder containing the files snps.csv and meta.csv, following the file format as described in section 1. Note that the download files has an extra column compared to the uploaded files, as they contain a unique identifier in order to separate several genotypes for the same animal.

History Table

The progress of both uploads and downloads can also be followed in the history table.

The table is by default sorted by date, with the most recent job shown first, but all headers can be pressed to change the sorting as you choose. The search field can be used to easier find specific jobs you may search for.

By clicking on the job-ID of the job of your interest, you will be re-directed to the status-page for that upload or download.

PSE File Formats

Submissions to GenoEx-PSE must be uploaded as a ZIP-archive containing two files: meta.csv (file702) and snps.csv (file704). 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. Note that SNP-names must be written in capital letters.

At each upload from a Service User, both files must be zipped together and submitted at the same time. Data submitted in one file will not be processed until both files are available .

Data extracted from the GenoEx-PSE database generally follow the same format as the data uploaded. The downloaded files does however contain one additional column with a Unique Upload ID, allowing to match meta.csv and snps.csv files coming from different uploading events. Therefore, Upload ID allows distinguishing multiple records of one individual coming from different sources and/or genotyping events. If you wish to upload more than one genotype for a given animal, you will have to do it in a separate set of files, as the database does not accept any duplicates in order to allow distinguishing between various genotyping events.

! Please note: Since the input files are comma delimited, do avoid the use of comma within a data field. If any of your fields require comma sign, add the escape character ‘\’ before the comma e.g. ‘Laboratory\, Branch’.

file 702 - meta.csv

File 702, named meta.csv, is required to be a variable length, comma delimited file in .csv format including a single record for each animal for which a SNP genotype details is being reported in the snps.csv file. For example, if the snps.csv file (File 704-AB or 704-TOP) includes SNP genotype results for 100 animals, the meta.csv file will have 100 records, one per animal.

Col	Name	Format	Description	Example
1	Record type	Numeric	Record type	702
2	Service user	Alphanumeric	Name of uploading organisation	INRA
3	Source country/sending country	Alphanumeric	3 letter country code²	FRA
4	Animal ID¹ - breed code	Alphanumeric	3 letter breed code³	BSW
5	Animal ID¹ - country code	Alphanumeric	3 letter country code²	AUS
6	Animal ID¹ - sex code	Alpha	1 letter breed code, M or F	M
7	Animal ID¹ - registration	Alphanumeric	Animal identification, maximum 18 characters	0001234567
8	Genotyping Laboratory	Alphanumeric	Genotyping laboratory⁴	Weatherbys Ireland
9	Sample ID	Alphanumeric	Sample numbers used in the genotyping laboratory	R1234567890
10	Scan Date	Numeric	date when laboratory concluded the analysis, format yyyymmdd	20220425
11	Platform	Alphanumeric	SNP platform⁵	Illumina
12	SNP array	Numeric	SNP array, named by number of SNPs⁵	54001
13	Call Rate	Numeric	Percent call rate of the animals full genotype used to create the SNP record for GenoEx-PSE, two decimals	99.98
!downloads only!
(14)	upload ID	Alphanumeric	Unique ID allowing to match multiple data files of the same individual by upload event	1fdb3a18-4a0d-41ee-8530-dac3880d00cf

file 704 - snps.csv

File 704, named snps.csv, contains the actual genotype data for the animals listed in the corresponding meta.csv file.

The Service User may select to upload and/or download SNP genotype data in either the "AB" or "TOP" allele designations, which determines the content of the first field, namely Record Type, in the following file format (i.e.: File 704-AB versus File 704-TOP, respectively). The file704-AB/704-TOP will be exchanged as a variable length, comma delimited file in .csv format and include a single record for each SNP included for each animal.

For example, if meta.csv file includes 100 animals and each SNP genotype include the 200 SNPs recommended by ISAG for Parentage Verification then snps.csv will include a maximum of 20,000 records (100 animals x 200 SNPs each). In the event that any SNP was not "called" and the result is missing, then that SNP for that animal should not be included in the GenoEx-PSE genotype exchange file. For this reason, even if the meta.csv file includes 100 animals, this second file may not necessarily have a total of 20,000 records.

Col	Name	Format	Description	Example
1	Record type	Numeric	Record type	704-AB or 704-TOP
2	Animal ID¹ - breed code	Alphanumeric	3 letter breed code³	BSW
3	Animal ID¹ - country code	Alphanumeric	3 letter country code²	AUS
4	Animal ID¹ - sex code	Alpha	1 letter breed code, M or F	M
5	Animal ID¹ - registration	Alphanumeric	Animal identification, maximum 18 characters	0001234567
6	SNP Name	Alphanumeric	SNP Name in CAPITAL letters⁶	ARS-BFGL-BAC-19454
7	Allele 1	Alpha	A/B for 704-AB, A/C/G/T for 704-TOP	A
8	Allele 2	Alpha	A/B for 704-AB, A/C/G/T for 704-TOP	A
!downloads only!
(9)	upload ID	Alphanumeric	Unique ID allowing to match multiple data files of the same individual by upload event	1fdb3a18-4a0d-41ee-8530-dac3880d00cf

¹Columns 4,5,6, and 7 does together make up the animal identification. Interbull ID is not a requirement in PSE, but it is highly recommended to be used for animals that has such identification. For further information on Interbull ID, see ID guidelines
²Country code according to ISO country codes
³Breed code according to ICAR breed codes
⁴Allowed values according to laboratory list. To request inclusion of new laboratories, e-mail Interbull Center at genoex@slu.se prior to upload
⁵Allowed values according to platform/array list. To request inclusion of new platforms or arrays, e-mail Interbull Center at genoex@slu.se prior to upload
⁶Full SNP list for parentage verification and parentage discovery