Publishing germplasm data through Genesys

We describe in this section the processes and tools available for publishing your plant germplasm data through Genesys.

Genesys currently supports two types of germplasm derived data: passport and characterization and evaluation data.

Establish institutional agreement

Once your institution has decided to share data through Genesys, we will provide you a template of the latest version of the Genesys Data Provider Agreement. This agreement is the instrument that confirms that your institution wants to publish data through Genesys, and explains the terms and conditions for publishing data through our portal.

Publishing passport data

1. Map your database to the Multi-Crop Passport Descriptor (MCPD V.2.1)

Genesys uses the FAO/Bioversity Multi-Crop Passport Descriptors Version 2.1 (MCPD V.2.1.) as a standard for data management and exchange. Read carefully the descriptions of each component of the MCPD and map it to your database. The more fields are mapped to the MCPD, the better documented your accessions will be.

Genesys uses the Passport Descriptor Completeness Index (PDCI) as an quality indicator of passport data. Make sure your passport data is complete to obtain high PDCI scores.

2. Check your data

Use the Genesys Validator for checking the spelling of the scientific names and the accuracy of geographic coordinates of each passport record to be published on Genesys. This process will help you to check the quality of your data, identify needs for improvement, and make your data reliable for others.

• Taxonomic names: The Genesys Validator compares all the scientific names you provide against GRIN Taxonomy, a taxonomy widely accepted within the plant genetic resources community, and identifies whether the scientific names are well-spelled, up to date and accepted.
• Geographic coordinates: The Genesys Validator checks geographic coordinates in two different ways. First, it overlays the geographic coordinates on a global map to identify if the coordinates are mapped on land or sea. Second, it cross-checks if the latitude and longitude match the country of origin provided (See Hijmans et al, 1999 for a explanation of geographic coordinates cross-check).

3. Choose tool for uploading data

You can push your data to Genesys either by using the Genesys API (See reference manual), or by using Genesys Anno, the standalone application. Genesys Anno is available for download here: Windows and macOS (See user manual).

4. Upload data to test server

We highly recommend you to first upload your data in our sandbox, to test and check how your data would look when published. This step can also help you to make corrections in your data (if needed!).

5. Upload data to production server

Once you feel your data is ready for being published through Genesys, upload it to our production server.

Publishing characterization and evaluation (C&E) datasets

Genesys maintains a section for publishing characterization and evaluation data of genebank accessions. This section is called the Genesys Catalog. Here data publishers can document the crop descriptors used for producing their C&E datasets and basic metadata that describe the context in which the datasets were produced.

Unlike passport data publication, the Genesys Catalog allows data publishers to login, register and manage their datasets using a web interface.

1. Check if your C&E dataset descriptor list is registered in the Genesys Catalog

The Genesys Catalog maintains descriptors lists for more than 20 crops, including banana, maize, rice, potato and barley. Before registering your dataset, you will need to check if the descriptors in your C&E dataset are already available in the Genesys Catalog.

If the crop descriptors of your dataset are not available in the Genesys Catalog, you will need to login the Genesys Catalog web interface and create a descriptor list. Here you will be provided with a template that will help you to upload your descriptors in batch.

2. Register your C&E dataset

Once you make sure your descriptor list is registered in the Genesys Catalog, you can proceed to register your dataset. For this you need to login and select the create dataset option in the dashboard.

In this section you will be asked to provide basic information about your dataset. This process consists of seven steps:

1. Basic information
2. Dataset attachments
3. Dataset creators
4. Timing and location
5. List of accessions
6. Traits observed
7. Review and published

3. Publish dataset to the Genesys Catalog

Once you review and consider that your dataset is ready for being published, you will only need to hit the accept and publish button.