Genesys

Full-text search

Finding information about a particular record in a large database can be exhausting for users. We wanted to design the platform so that a user can find an accession in a simpler way. Elasticsearch turned out to be a great solution that allows for full-text search and filtering for specific values.

Visualization with interactive maps

Taking into account that the human brain perceives visual content easier than long tables of dry data, we needed a modern Javascript solution for interactive maps that can integrate with Genesys APIs.

Using the open-source Leaflet library we implemented a map-based search for users to explore the provenance of crops.

The map shows locations of where the samples of crops were originally collected. Users can select a place on the map with an Area selection button and see locations mapped with green spots. After filtering accessions, a map with selected accession indexes associated with a particular area will appear before them accordingly to the required area or across the globe. A user is referred to the accession details page by clicking on the index.

Users can set a specified location of provenance knowing accession geodata as latitude and longitude and can select an area to find out which cultivars were originated there. Each accession contains information about its origin, soil, climate, in which climatic environment it was originally grown, etc.

Thus, from an ordinary map, it turned to a visual display channel for users, helping get the information more easily.

Filter by climate

Where plants thrive is heavily influenced by the climatic conditions: precipitation, temperature, wind, etc. This is an important factor for breeders when selecting material.

Many cultivars grow in several locations worldwide in a similar climate to that of the place of origin. That’s why we implemented a function where users can search for accessions based on the climatic parameters of their origin.

Users can configure the map, setting the preferred temperature and precipitation values with a slider. We added twelve essential climate layers with current and future climate conditions based on global climate data from WorldClim.org. Users can configure the map layer transparency, putting one layer over another to see their correlation. For example, if users put on the temperature layer and a slightly transparent precipitations layer above it, they can visualize selected climate conditions.

Map configuration

By clicking on the Accession list button at the bottom, users are redirected to the list of accessions sourced from the locations of the selected climate conditions. You can see all the details neatly structured in one place by clicking on the accession.

Now you can look into the complete information and choose a sample for request. Users can sort cultivars by climate conditions and see climate visually at the origin with precipitation on colorful diagrams.

Saved filters and maps

Everybody knows it’s tedious having to check off filter settings again and again. We tried to provide users with a shortcut to finding what they are looking for.

The ability to save filtered content in the browser reduces the search time of users. That’s why we made it possible to save accession filter settings in order not to set up again when the browser is reopened. The same feature is available for climate maps.

My list

Researchers and breeders can request samples of cultivars from select genebank. Users can add entries to their list by selecting the holding institute and the list of accession numbers of interest. They can request multiple accessions from different genebanks at the same time.

Another way to select accessions for the request is finding them on the map. The map-first way of search allows starting with geo conditions, which is a decisive factor for many breeders.

Image handling

Unoptimized image quality and size result in high bandwidth usage while browsing the website. We introduced gradual image resampling from high to low resolutions for thumbnails served by the website.

The visibility sensor helps determine when a user is ready to see more images of samples and calls algorithms to action. This prevents fetching images that are not visible on screen. We made it work smoothly without long loading times for users.

Genesys API

Curating data about crops in a genebank is a labor-intensive and noble cause at the same time.

How do we engage institutes in data sharing? By providing them with solutions that simplify the process.

The Genesys platform offers APIs and allows using a Java-based Anno upload tool for quick data contribution. We made the Anno app downloadable to convert users’ Excel, CSV files and database SQL queries to Multi-Crop Passport Descriptor format (MCPD). After that, saved data goes to the Genesys platform for publication.