More features added in August!
12 September 2023
Read about the upgrade of the traits search, quick download option, and the new curation type descriptor added to Genesys in August 2023.
Searchable trait datasets levels up
In case you missed the update from May this year, Genesys started unpacking raw characterization and evaluation data, making them searchable directly on the platform through dynamic filters and visualizations. You can access the documentation on this feature in the how-to use article, or a brief summary through the tweet on social. This was made possible through a change to the publishing process: Genesys enables the genebanks to validate and map trait data to the correct descriptors as part of the uploading of trait data in Genesys.
This feature is now taken one step further, and allows you to search across many different datasets belonging to the same genebank or crop.
Let’s take the example of the trait data of the World Vegetable Center. The center has published 13 datasets in Genesys over the years, and has recently updated some of them to make them individually searchable. Since the August update, users can search through these datasets all at once, having the option to filter the accessions by passport data in addition to trait data.
All you have to do is navigate to the passport data browser, and use the filters pane on the left hand side to narrow the 4M+ accessions in Genesys down to the accessions from WorldVeg, by filtering for TWN001 in the filter titled Holding Institute. You can also narrow this search furhter down by crop, taxonomy, provenance, and so on. You have at your disposal all the passport data filters, including climate variables, documented in this article.
Once you have defined your passport data filters and pressed on Apply Filters in the left pane, toggle to the Traits tab (step 1). This will load the descriptors associated with trait data from WorldVeg. The descriptors that do not indicate a crop name next to them are cross cutting (step 2), while the ones that do are crop-specific (step 3).
Then you may scroll down and select the descriptors you want to filter for, for example Blossom end scar condition (step 4). In this case Genesys returns all the accessions that have this descriptor associated with them. If you want to be more specific, you may expand one descriptor (step 5) and select the specific traits for it, for example Blossom end shape indented and pointed (step 6). Then click on Apply filters at the bottom right of the page to filter for these traits or descriptors.
Genesys then returns all the accessions associated with the traits and descriptors you filtered for, and you may adjust your search at any point by clicking on the orange ribbon to return to the list of trait filters (step 7).
Quick download option for passport data
As you probably already know, the data published on Genesys follows the Multi-crop Passport Descriptors (MCPD) standard, which includes around 26 different descriptors. Passport data can be downloaded in Darwin Core or Excel format for up to 200,000 accessions (step A).
The Quick download allows you to select individual descriptors you wish to download instead of the entire MCPD list. The download is possible for up to 1,000,000 accessions at once (step B). Genesys returns a CSV file that you may convert to Excel or import to a data analysis software. The main benefit of the Quick download is the speed at which Genesys will produce the resulting CSV. For the same number of accessions, the CSV is generated in a matter of seconds, while it may take a few minutes for Genesys to compile the same data into Excel format.
Curation type added to passport data
The Guidance Note for CGIAR Genebanks on Improving Accession Management, published in 2022 as part of the Genebank Platform, requires genebanks to specify the type of curation of each accession in their collection.
The four curation classes are: Fully curated, Partially curated, Archived, and Historical. Each class of curation represents a different level of activity provided by the genebank in the curation of the materials concerned.
The descriptor is now available in Genesys. Stay tuned for the CGIAR genebanks to include this data in their updates!