WhereNext wins 2019 GBIF Ebbe Nielsen Challenge

Open-source system developed by Jorge Velásquez-Tibatá of Colombia optimizes site selection to fill gaps in biodiversity data, tops slate of nine winners in annual incentive prize

Spatial ecologist Jorge Velásquez-Tibatá developed WhereNext, the first prize winner in the 2019 GBIF Ebbe Nielsen Challenge.

Colombian spatial ecologist Jorge Velásquez-Tibatá of The Nature Conservancy has won first prize in the 2019 GBIF Ebbe Nielsen Challenge for developing Wherenext, an open-source web-based system that recommends target areas for biological surveys and data mobilization.

WhereNext is an interactive web application that builds on existing tools, data and services to optimize the process of comparing, selecting and filling biodiversity data gaps. Once users have selected a taxonomic group and region of interest, the app produces models that recommend new survey areas based on expected differences in the species communities present in different environments and habitats.

This approach, known as Generalized Dissimilarity Modeling (see Ferrier et al. 2007), can identify sites that are less similar biologically to other previously sampled sites. The resulting areas are potentially the best candidates for complementing existing surveys, prioritizing data mobilization and even finding species new to science.

”I envision people using WhereNext to plan new biological expeditions or citizen-science surveys that complement existing knowledge best while revealing and protecting undescribed biodiversity”, said Velásquez. ”I drew inspiration from existing sampling initiatives in my country and wondered how to create a data-driven system that optimizes site selection with enough flexibility to account for field contingencies like accesibility.”

Velásquez hopes to to collaborate with other scientists to develop future releases of this R package and Shiny app to pull in environmental data from additional global repositories and improve support for analysing very large datasets.

As this year’s first-place winner, Velásquez will receive €10,000 from a total prize pool of €32,500.

Three teams share second-prize winners, and five more finish joint third

This year’s jury selected three more teams as joint second-place winners, and each will receive a €5,000 prize.

occCite: Tools to Enable Comprehensive Biodiversity Data Citation is a a set of R-based tools for downloading, managing, summarizing, and citing biodiversity data, to complete the data citation cycle. Developed by Hannah L. Owens of the Center for Macroecology, Evolution and Climate, GLOBE Institute, at the University of Copenhagen and four U.S.-based colleagues—Cory Merow of the University of Connecticut, Brian Maitner of the University of Arizona, and Vijay Barve & Rob Guralnick of the Florida Museum of Natural History—this toolset preserves links between occurrence data and primary providers throughout data processing workflows with the aim of acknowledging and encouraging primary data providers to continue the hard work of contributing open data.

Organella offers an experimental user interface that gives non-specialists and beginners playful and visual ways to access and explore biodiversity data. The team of Andrea Biedermann, Diana Gert, Dimitar Ruszev & Paul Roeder of the University of Applied Science Potsdam in Germany created these new forms while exploring patterns of data visualisation and interaction design that operationalize data without relying on conventions like dropdown lists, text inputs and sliders.

Rapid Least Concern: Automated assessments of lower risk plants for the IUCN Red List of Threatened Species (Red List) presents a repeatable, auditable and scalable approach for speeding and scaling up the assessment of plant species in light of the current biodiversity crisis. Developed by Steven Bachman, Barnaby Walker and Justin Moat of Royal Botanic Gardens, Kew in the United Kingdom, ’RapidLC’ automatically generates all data required for an IUCN Red List-compliant Least Concern assessment, expediting the Red Listing process for plants and offering a potential approach to other megadiverse groups such as fungi and invertebrates.

The jury also named five more teams as third-place winners, each of which will receive €1,500. These submissions are described below.
Agile GBIF Publishing
Biodiversity Information Review and Decision Support: the BIRDS package for R
GB Sifter: A GBIF to GenBank Data Sifter
GeoNature-atlas: Publish an online biodiversity atlas with GBIF data of your area

The Ebbe Nielsen Challenge is an annual incentive prize that honours the memory of Dr Ebbe Schmidt Nielsen, an inspirational leader in the fields of biosystematics and biodiversity informatics and one of the principal founders of GBIF.

2019 GBIF Ebbe Nielsen Challenge prizewinners

First Prize winner

WhereNext: a recommending system to identify sampling priorities based on generalized dissimilarity modeling

WhereNext is an R package and shiny app that guides users through the process of developing a GDM for arbitrary taxonomic groups and regions and interactively recommends sites that complement the most existing surveys. To build GDMs, it connects to global biodiversity data (GBIF) and other environmental repositories (WorldClim) and offers tools to improve data quality by implementing occurrence data cleaning routines and environmental variable selection procedures, as well as to identify sites with complete surveys.

Second Prize winners

occCite: Tools to Enable Comprehensive Biodiversity Data Citation
OccCite is a set of R-based tools for downloading, managing, summarizing, and citing biodiversity data, to complete the data citation cycle. These tools preserve links between occurrence data and primary providers throughout R-based data processing workflows. OccCite also facilitates primary data provider citations in peer-reviewed manuscripts and other publications. The team hopes their efforts ensure primary data providers receive credit for the hard work they put into assembling and publishing data, while encouraging them to continue to contribute to ongoing data aggregation efforts.

The team originally created this experimental user interface for data from the GBIF network in a seminar on data interfaces. Inspired by the challenge of giving beginners playful and visual access to critical information for addressing global environmental challenges, Organella allows users without specialist knowledge of biology or taxonomy to manipulate, engage and understand complex biodiversity data.

Rapid Least Concern: Automated assessments of lower risk plants for the IUCN Red List of Threatened Species (Red List)
The comprehensive process of assessing the extinction risk of plants under the IUCN Red List remains a limiting factor in species conservation, given that the annual rate of assessment barely matches the rate of newly described plants. RapidLC provides a repeatable, auditable and scalable workflow for expediting production of IUCN Red List Least Concern assessments for plants. The tool accesses data feeds from both GBIF and the Plants of the World Online (a critical taxonomic resource maintained by Royal Botanic Gardens, Kew) and generates metrics that can accurately determine if a species is likely to be Least Concern or not. RapidLC then automates documentation of ‘Least Concern’ species, in effect fast-tracking these assessments so that highly trained Red List assessors can focus their efforts on species expected to be under threat. RapidLC also highlights the potential for applying this approach to other megadiverse and under-assessed groups like fungi and invertebrates.

Third Prize winners

Agile GBIF Publishing
This module for EarthCape platform reduces barriers to sharing research and collections data, enabling one-click publishing to GBIF via Zenodo directly from a personal database. In addition to the module allows researchers to publish their data without interrupting other workflows while eliminating the need of setting up an instance of the GBIF IPT or any other software or online presence.

Biodiversity Information Review and Decision Support: the BIRDS package for R
This package—produced by a team that includes the winner of the 2016 Ebbe Nielsen Challenge—facilitates an integrated review of spatial and temporal dimensions of a given set of primary biodiversity data. By exploring a number of variables related to sampling effort and coverage (data gaps), BIRDS systematically analyses and visualizes the data’s fitness-for-use, helping make decisions about its use in further analyses.

GB Sifter: A GBIF to GenBank Data Sifter
This R-based web application allow users to search for region- or taxon-specific records through the GBIF network, match them to several bioclimatic and ecological map layers, and then query phylogenetic markers for species of interest in GenBank. This workflow provides a method for exploring relevant open data infrastructure for studying trait evolution in phylogenetic and ecological contexts.

naturaList automates the process of classifying GBIF-mediated occurrence records based on six degrees of confidence in their species identifications. Users without taxonomic expertise can use the tool to improve the quality of the data and account for the scale of their analysis, filtering the records most fit for their purposes based on well-defined criteria.

GeoNature-atlas: Publish an online biodiversity atlas with GBIF data of your area
Building on earlier efforts to publish biodiversity data from French national parks, this team aimed to show how GBIF web services can support easy access to local biodiversity knowledge. Groups at any scale—countries, states cities—can publish an online biodiversity atlas allowing citizens anywhere to discover the richness of local biodiversity, the threats it faces, and the importance of preserving it.

Jury for 2019 Ebbe Nielsen Challenge

  • Greg Riccardi (chair), Florida State University
  • Peter Brenton, Atlas of Living Australia
  • Rachel Tierney, Scottish Wildlife Trust
  • Dave Martin, Atlas of Living Australia
  • Lars Francke, OpenCore
  • Dave Remsen, Marine Biological Laboratory
  • Roderic Page, University of Glasgow
  • Andre Heughebaert, Belgian Biodiversity Platform
  • Anders G. Finstad: Norwegian University of Science and Technology
  • William Ulate, Missouri Botanical Garden
  • Philippe Grandcolas: Centre National de la Recherche Scientifique | Muséum national d’Histoire naturelle
  • Jurate De Prins: Royal Belgian Institute of Natural Sciences
  • Eduardo Dalcin, Rio de Janeiro Botanical Garden Research Institute
  • Dag Endresen, University of Oslo Natural History Museum `| GBIF Norway
  • Anabela Plos, Argentine Museum of Natural Sciences (MACN-CONICET) `| GBIF Argentina
  • Paul Morris, Harvard University Herbaria and Museum of Comparative Zoology