By christelle.rabil@croptrust.org
21 February 2023

Read about the improvements and new features added to Genesys in January 2023.

The most exciting new feature in this update is intended for data providers – a new tool is available for genebank data managers to assist with the validation and publication of trait datasets. Don’t worry, the users also benefit from this development, and will have access to better documented trait datasets! The website also loads faster, and is optimized for better indexing and ranking in search engines.

For genebanks: Publishing trait datasets

Genebanks publish trait datasets and enable researchers to download the data files and associated trait descriptors from Genesys for their own analysis. The original process of publishing datasets, developed as part of the Genesys Catalog of Phenotypic Datasets project (2017-2019), required that genebank data managers manually annotate the dataset by selecting the traits and the list of accessions documented in the file.

The Dataset Validator extracts trait observations from the uploaded file, and allows the data manager to define a new trait descriptor based on values in the dataset, or to select an existing trait descriptor from the Genesys database of over 5,000 existing definitions.

Once the descriptor is selected, the tool ensures that every observation in the source file conforms to the descriptor definition, highlighting the values that fall outside the allowed range. Data managers can correct typos and re-map values with an automatic Guess function.

This new tool makes the documenting of datasets much more convenient for genebank data managers, facilitates descriptor reuse, and will hopefully encourage more genebanks to publish trait datasets in Genesys.

Downloading maps

Maps of accession collecting sites are frequently used in publications and blog posts, and to prepare the figure, one had to resort to taking a screenshot of the Genesys website, and manually edit the picture with an image editor. An alternative approach was to download a KML file and create the map using GIS software.

Genesys now provides a function to generate a print-quality image of the current map (in PNG format), ready for inclusion in your publication: click the Printer icon and choose the Download option. The image Scale option lets you set the image resolution, with higher scale generating a higher resolution image.

The maps are composed of layers, with the bottom layer displaying the World map, and the top layer displaying localities of accession collecting sites. The accessions layer is calculated dynamically based on your selected filters, and the current passport data in Genesys. This functionality is updated with improved capacity for Genesys to serve more concurrent users, considering that maps are also used in Embedded Genesys on various institutional websites.

A small update for Subsets and C&E Datasets

Genesys now displays the date when the subset (or dataset) was first published. Unlike the date of the last modification, this date does not change if the subset receives small editorial changes. One can also use the Published in Genesys filter (under Date search) to narrow the search to a specific period, for example to list subsets published in 2022 (i.e. between 1 January 2022 and 1 January 2023). The same applies for Datasets.

You can also create your own list of Subsets or Datasets using the corresponding Filters. For Subsets, look for the Subsets section in the filters, and use the autocompleter to pick the subsets to include in the list.  Once you hit the Apply filters button, Genesys generates a URL that embeds your filters and you can bookmark or share the link with others. The same applies for Datasets.

Integration with genebank systems

Genesys provides API endpoints through which genebank's internal information systems access and retrieve information about requests for material in their collections, made by Genesys users. From now on, these systems can also record, in Genesys, their internal order tracking numbers, informing Genesys that the request is being processed. GGCE is the first genebank information management system that uses the new functionality.

Taxonomic backbone

Genesys uses GRIN Taxonomy to provide a backbone to which accessions are linked based on taxa provided by genebanks. The updated Genesys is able to better resolve misspelled names, and stay in sync with the currently accepted names according to USDA taxonomists.

Done with Genesys?

Genesys automatically disables user accounts that are not accessed for more than 12 months. Unless reactivated by the user, we periodically remove such user accounts from Genesys, scrubbing any personally identifiable information from the database.

To give you complete control over your Genesys account, you are able to delete it yourself, if you so wish. You can remove your Genesys account under User profile in the Genesys Dashboard.

You are always welcome back to Genesys and can register a new account in the future.

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