Six finalists selected for GBIF Ebbe Nielsen Challenge

Publicerat av GBIF.org --


An expert jury has selected six highly innovative finalists from among 23 submissions received for the inaugural GBIF Ebbe Nielsen Challenge, inviting their creators to compete for €25,000 during the innovation prize’s second and final round.

The six finalists reflect a wide range of uses of open-access biodiversity data from the GBIF network. They range from browser-based insights on dataset quality to regional bird and frog soundscapes, and from a web application that provides interactive predictive modelling to social media-powered biodiversity assessments,

The winners (in alphabetical order) are:

Three teams and three individuals located in seven countries are responsible creating the six finalists (profiled briefly below). These entries vary widely in geographic scale, analytics and media integration, and all competition entries are available on the Challenge pages on ChallengePost.

“The creativity and ambition displayed by the finalists is inspiring’, said Roderic Page, chair of the Challenge jury and the GBIF Science Committee, who introduced the Challenge at GBIF’s 2014 Science Symposium in October.

“My biggest hope for the Challenge was that the biodiversity community would respond with innovative—even unexpected—entries,” Page said. “My expectations have been exceeded, and the Jury is eager to see what the finalists can achieve between now and the final round of judging.”

The six finalists, each of whom will receive a €1,000 initial prize, now receive an invitation to further refine their submissions while competing for €25,000 in prizes during round two of the Challenge. The first- and second-place winners—who will receive €20,000 and €5,000, respectively—will be announced at the GBIF Governing Board meeting (GB22) in Madagascar in October 2015.

2015 GBIF Ebbe Nielsen Challenge Finalists


Developed by Tom August
This service leverages location information from Twitter users who use the the hashtag #myGBIF—“One hashtag, infinite possibilities”, as August suggests. Functioning as a hyper-local personalized biodiversity assessment, the call to #myGBIF retrieves species occurrence data from the user’s area, mashes them up with common names and IUCN extinction risks via the Encyclopedia of Life, and promptly tweets a resulting infographic back to the user.
View submission


Developed by Richard Pyle
Biodiversity informatics needs reliable, persistent and actionable digital identifiers, but the community has made little progress toward resolving its glut of multiple identifiers and sources for any given data object. BioGUID.org provides a common service for indexing and cross-linking a wide range of identifiers, making it easier to cross-link biodiversity datasets, and making them more powerful by harnessing identifiers.
View submission


Developed by Miguel Porto
Promising “a new way of looking at species occurrence datasets”, this dynamic web application lets users navigate the relationships within regional species groups that are displayed as an ecologically meaningful network. Its interactive interface shows species’ ecological or biogeographical affinities based on user-selected bioclimatic variables and expands at each step to reveal the network’s complexity.
View submission

GBIF dataset metrics

Developed by Peter Desmet, Bart Aelterman & Nicolas Noé
This team has created a ready-to-use browser extension for Google Chrome, offering quick insights about the datasets available through GBIF.org. Its chart-based visual approach provides at-a-glance assessments of the occurrences contained in a dataset, enabling a user to assess its fitness for his or her use without having to download, filter and clean the data.
View submission

GBIF Soundscape

Developed by Ben Raymond & Peter Neish
This application taps the rich if unconventional stream of information available in sound recordings associated with some occurrence records. Drawing on the GBIF API, it reconstructs the natural "soundscapes" using audio files associated with bird and frog occurrences in selected regions.
View submission

Wallace (beta v0.1): Harnessing Digital Biodiversity Data for Predictive Modeling, Fueled by R

Developed by Robert P. Anderson, Matthew Aiello-Lammens, Bob Muscarella, Bruno Vilela & Jamie Kass
This submission combines data from the GBIF network with two recently developed tools developed in R, a high-powered programming language for statistical computing and graphics, allowing users to generate predictive distribution models. The web application enables researchers working online or offline to map, filter and remove occurrence records and build, evaluate and visualize complex predictions.
View submission

New GBIF fund targets biodiversity information needs in Asia

Publicerat av GBIF.org --


A new fund aims to supplement existing activities of GBIF to support the needs of researchers and policymakers in Asia through mobilization and use of biodiversity data.

The Biodiversity Information Fund for Asia (BIFA) is the outcome of a contribution to GBIF supplementary funds of more than €156,000 from the Japanese government, earmarked for activities in the Asia region.

Allocations from the fund may support the following broad areas of activity:

  • Partial support for a meeting of the regional subcommittee for Asia of the GBIF Participant Node Managers Committee
  • Support for activities aimed at enhancing biodiversity knowledge at the regional level—for example, generating species checklists—based on priorities agreed by GBIF nodes in Asia
  • Support for capacity-related activities in Asia, such as mentoring and training workshops
  • Support for GBIF-related activities potentially contributing to the work of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), in particular the upcoming regional assessment of biodiversity and ecosystem services for Asia and the Pacific

A steering committee comprised of representatives from the Ministry of the Environment, Goverment of Japan, the Asia regional group of GBIF nodes, and the GBIF Secretariat will determine the use of the fund within these areas. More information on the allocation of funds from BIFA will be available on GBIF.org in the coming months.

“The establishment of this new fund demonstrates the commitment of the government of Japan to support the mission of GBIF in Asia,” said Donald Hobern, GBIF Executive Secretary. “We hope and expect that the activities supported by BIFA will add significantly to the ability of Asian researchers and decision-makers to access the data required for better understanding and management of the region’s biodiversity.”


Molecular-Clock Dating Using MrBayes – Seminar and Workshop

Publicerat av Johan Nylander --

Molecular-Clock Dating Using MrBayes – Seminar and Workshop

  • 22 April – Stockholm: 09:30-11:30, Rum 540, Botaniska Institutionen, Stockholms universitet
  • 23 April – Uppsala: 13:15-15:15, Lärosal 4, Evolutionsbiologiskt Centrum, Uppsala universitet

Chi Zhang*, Swedish Museum of Natural History, Stockholm
Johan Nylander, BILS/Swedish Museum of Natural History, Stockholm

MrBayes – the most often used software for Bayesian phylogenetic analysis – has included many new features since version 3.2. In this seminar, we will highlight some newly implemented functionality, with focus on the molecular-clock dating capacities of the current version (v.3.2.4). The seminar will consist of two parts, where following a presentation* giving the necessary backrground information, there will be a hands-on tutorial where participants are encouraged to bring their own data (and computers).

There are two approaches on dating using molecular data: node dating and total-evidence dating. Node dating calibrates the internal nodes of the tree by assigning distributions using information from external sources, such as the fossil record. Total-evidence dating uses the morphological data from fossil record and morphological and sequence data from recent organisms together to infer the dates. Several steps involve in Bayesian dating analysis, including data partitioning, node or fossil age calibration, and setting priors for the tree and the molecular clock model. I will describe the available calibration probability distributions, clock tree priors – especially the fossilized birth-death prior for total-evidence dating, and relaxed clock models, through a step-by-step tutorial of MrBayes.

The program (MrBayes v.3.2.4) is available from http://mrbayes.net (alternatively https://sourceforge.net/projects/mrbayes/files/mrbayes)

Participants in the practical part are encouraged to bring their own computers with the software installed from the above mentioned URL’s.

Software release supports consistent DOI-based citation

Publicerat av GBIF.org --


The GBIF Secretariat has published version 2.2 of its Integrated Publishing Toolkit (IPT), a free open-source software tool for publishing and sharing biodiversity data. The new version supports consistent, traceable attribution of GBIF-mediated data and downloads, streamlines how publishers define appropriate uses of their data, and improves data quality control.

IPT v2.2 introduces the use of digital object identifiers (DOIs) for datasets, which gives users a stable, easy-to-use model for citing data sources. This approach also improves publishers’ ability to track how and where users apply their data, in both research and web applications. Updates to GBIF.org also support this new citation model,by displaying DOIs both for datasets and for user downloads. Since early February, GBIF has issued DOIs for all newly published datasets (example 1), and GBIF.org now recognizes and displays publisher-assigned DOIs for existing datasets (example 2).

User downloads also now receive GBIF-issued DOIs. This approach significantly simplifies references to any and all datasets represented in user-defined search results, even complex ones comprising occurrences from many different datasets.

The new IPT release also introduces standardized machine-readable data licenses, emphasizing GBIF’s commitment to open access.

Publishers upgrading to IPT v2.2 will have to choose to share new datasets under one of three Creative Commons licenses: CC0, CC BY or CC BY-NC. Publishers who wish to keep non-CC license conditions can continue to publish data using the previous version of the IPT, and the Secretariat will continue to welcome feedback on their concerns about the new licensing options.

These licences provide a consistent way for publishers to define appropriate uses of their data. GBIF will encourage them to adopt the least restrictive terms possible to encourage the widest use and application of their data. This development represents the culmination of an extensive community-driven consultation process and implements recent decisions by the GBIF governing board.

Finally, IPT v2.2 introduces stricter quality control around the Darwin Core standard’s basis of record. As a result, the software will alert publishers when data records fail to distinguish the specific nature of the occurrences, such as specimens, literature citations and observations.

Work is already underway for IPT v2.3, which will introduce support for publishing sample-based datasets and displaying through GBIF.org.