GenoEx- PSE – User's Manual

This document describes the procedures for the upload and download of the data for the GenoEx-PSE service.

It describes in details required file formats, login process and usage of the service itself both for data upload and 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.

Login

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.

More information about allowed values in PSE-files can also be found here:

• PSE File Formats

• Breed codes

• ISO country codes

• Platform arrays

• Laboratories

• Parentage verification SNP

• Parentage discovery SNP