Explore the traits in WoRMS and Aphia with a brand-new R Shiny application | Lifewatch regional portal

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Explore the traits in WoRMS and Aphia with a brand-new R Shiny application

Added on 2023-01-30 16:24:45 by Dekeyzer, Stefanie
With this new R Shiny application, you can explore all trait information in the World Register of Marine Species (WoRMS) and its underlying Aphia database in a more advanced way, for instance by combining different traits and combining traits with standardized distributions.
The importance of describing species patterns and the underlaying processes explaining these patterns is essential to assess the status and future evolution of marine ecosystems. This requires biological information on functional and structural species traits such as feeding ecology, body size, reproduction, life history, etc.

The World Register of Marine Species (WoRMS) aims to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. Next to taxonomic information, WoRMS and Aphia, its underlying SQL platform, can hold non-taxonomic information such as distributions, traits, images, etc.

Within WoRMS, basic trait information, such as environment (marine-brackish-freshwater-terrestrial), was being collected before 2014. Since then, collecting trait information has been taken one step further within the EMODnet Biology project and as a component of the LifeWatch Species Information Backbone.

Now, information on a whole range of traits is being collected within WoRMS and Aphia. Three main types of traits are documented: 1) Biological and ecological traits-specific characteristics of a taxon (e.g., body size or feeding type); 2) Taxonomic traits (e.g., paraphyletic groups); and 3) Human-defined traits (e.g., Red List species). For an overview of all traits currently available in WoRMS and Aphia, with their definitions, see here.

The current Marine Species Traits Portal only allows to search for one trait at a time. With the new R Shiny application, the traits data in WoRMS/Aphia can be explored in a more advanced way:
  • Select the taxon (species level or higher) you are interested in; you can only select one taxon at a time. If the taxon does not appear in the picklist, then it means we don’t have any traits available for that taxon. Check "Include traits from child taxa" if you want to return all children of your chosen taxon.
  • Depending on the taxon you selected, a list of available traits will appear. You can select a single trait or a combination of traits for your chosen taxon. If you select two (or more) traits (e.g., macrobenthos and mobile), then the explorer will look for the taxa that are either macrobenthos or mobile (“ANY of selected traits”). If you want to look for taxa that have both traits, then check “ALL of selected traits”. You can also restrict your search to a specific life stage (e.g., adult, larvae).
  • You can combine the selected traits with standardized distributions based on distributions from literature in WoRMS and occurrences in OBIS. This way you can create a list of species which occur in a certain area, and which have a certain trait (e.g., all meiobenthos Nematoda species in the North Sea). The explorer is not able to give a list of all species within a certain area. Always use the standardized distributions filter in combination with the traits filter.
  • Every parameter is shown in a separate column in the data table. Select “Add classification” if you want to include the higher taxonomic classification to your results. “Compact traits in one row” is unchecked by default. If you check this box, the SourceID column is dropped and same values in one column are taken together where possible. Checking this box slows down the querying process, however.

The new R shiny application was added as an extra menu item on the current Marine Species Traits Portal (Data explorer). For the direct link to the new Data explorer, see here.

This work is supported by LifeWatch Belgium, part of the E-Science European LifeWatch Infrastructure for Biodiversity and Ecosystem Research. LifeWatch is a distributed virtual laboratory, which is used for different aspects of biodiversity research. The Species Information Backbone of LifeWatch aims at bringing together taxonomic and species-related data and at filling the gaps in our knowledge. In addition, it gives support to taxonomic experts by providing them logistic and financial support for the organization of meetings and workshops related to expanding the content and enhancing the quality of taxonomic databases.

Image by vectorjuice on Freepik.

Explore the traits in WoRMS and Aphia with a brand-new R Shiny application

Link: https://rshiny.vsc.lifewatch.be/traits-data/

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