GDE_logo.png 2020-Aug-10

GenoEx - GDE User’s manual v.1.0

part 2 – Database Manual

GDE stands for Genomic Data Exchange and GenoEx-GDE is the database that allows users to exchange whole SNP sets, where users define how and with whom the data is to be shared.

The whole system consists of the database itself, where data files can be uploaded and downloaded from, and the input files’ preparation program – gxprep.

The instructions for preparing the input files from raw laboratory files and for assigning sharing permissions can be found in the first part of this manual - gxprep.py preparation program.

This manual describes step by step how to:

1. Upload file formats

GenoEx-GDE allows upload of two types of files

Detailed file formats can be found in the first part of the manual, describing the usage of gxprep program. Here we only remind the examples of these files.

706 example

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

711 example

711;BSW;AUS;M;000000A12345;09c98b1e-6af8-4254-9768-58d7cd1ddafd;54609;ITBC,BFRO

2. Organizations, Users and Logins

Every organization which signs the contact for becoming GenoEx-GDE Service User is from the service’s point of view considered as single User. On the other hand, it is possible to create several separate personal logins for different persons within the organization. As one Service User, they share the History of uploads and downloads as well as all rights and permissions assigned to the User. New logins can be added to the Service User’s account at any point of time. To do so, the user should send the request to genoex@slu.se

At the login page, every person should log in with their personal credentials.

gde_login.png

3. GDE data upload

As part of GenoEx services, GDE is sharing the entry point with PSE, therefore please make sure that you choose the right tab for the upload in the drop-down menu.

genoex_start3.png

GenoEx-GDE allows for simultaneous or separate upload of 706 and 711 files. Choosing different alternatives results in one of the following scenarios:

In order to upload the file to the database, please choose the correct file from your computer and press UPLOAD

GenoEx_GDE_upload1.png

When upload starts, you will be redirected to the status page.

Note: this page does not update automatically, thus you must refresh it in order to see the progress.

init.png

The first status you will see is INITIATED, then PROCESSING and finally either FINISHED or FAILED, dependently whether the upload was successful or not.

gde_finished1.png gde_Uerror2.png

Like in the example above, FAILED is always accompanied with the informative error message, which allows the User to find and correct the problem.

In any case, the User will receive an e-mail when the data processing is finalized.

4. GDE data download

In order to download the User has to select the Download options from GDE drop-down menus.

The genotypes to be downloaded can be chosen by breed, country of origin, gender and chip used for genotyping. The User is also able to choose if to download all the genotypes available for the animals within chosen criteria (Full Extraction) or only one per animal, with the highest call rate.

gde_extr2.png

In here as well, the status page should be reloaded to see the current status. When the extraction is ready, a link to download the genotype file is provided:

gde_extr_compl2.png

The downloaded file is formatted according to 706 specifications. That also mean that corresponding SNP order file is needed to decode the 706 genotype string.

SNP order files download

If the User has already prepared the upload data with the same SNP order file than the downloaded data, the relevant SNP order file was saved in the defined directory (see GenoEx - GDE User’s manual part 1, section 2.1. parse). Otherwise, the SNP order file can be downloaded via the GDE Download tab.

5. User’s History

All the User’s actions as saved and can be later reviewed by them. As mentioned in section 2, GenoEx considers an organization that has a User’s Contract with Interbull Centre signed, is considered as single User, which however, can have several logins. The History is User, not Login specific, thus actions from all logins within one organization are listen in the history together.

gde_history2U.png


If you have any further questions and/or suggestions for improving this manual, please contact us at genoex@slu.se

public/GDE_user_manual (last edited 2020-08-31 15:40:08 by JoannaSendecka)