New opportunity for publication of species sampling and monitoring data

Publicerat av GBIF.org --


The international body responsible for maintaining standards for the exchange of biological data has ratified changes that improve support for mobilization and access of sample-based species data through the GBIF network.

By adding to the rich set of terms already available in the Darwin Core (DwC) standard, this action by Biodiversity Information Standards—also known as TDWG—will help GBIF-mediated data move beyond “presence only” data and support the discovery and application of richer, more quantitative information used in other areas of scientific discovery and research, particularly ecological monitoring and assessment.

Sample-based data come from thousands of different kinds of environmental, ecological, and natural resource investigations. These events range from one-off surveys to ongoing monitoring and include activities like freshwater and marine sampling, plant cover and vegetation plots, and citizen science bird counts, among others.

In addition to bringing in new datasets, these changes could also improve the quality and utility of many datasets already published through GBIF, which derive from the more complex sources required to understand how species populations change across space and time.

“The Darwin Core extension for sample data is a major advancement for the global biodiversity community,” said Henrique Pereira, chair of GEO BON. “Monitoring biodiversity change often requires repeated measures at the same place. This extension will enable data holders publishing through the GBIF network to share population abundance data (including time series population data) or presence/absence data, and also to document the sampling protocol.”

Because of their quantitative and calibrated nature and precisely described methods, sample-based data are better at detecting changes and trends in populations than the ‘presence-only’ observation and collection occurrences that make up much of today’s open-access biodiversity data. As a result, sample-based data are critical to understanding the prospect and pace of widespread global change.

The challenge in sharing sample-based data has been that the underlying data is often complex and difficult to encode in a relatively simplified data model. But over the past two years, the GBIF Secretariat has been working with EU BON partners and the wider community to identify additional terms for the Darwin Core vocabulary and enable support of sample-based data in the Integrated Publishing Toolkit (IPT). The aim is to demonstrate a new means of exposing datasets to maximize their discoverability and reuse, rather than prescribing methods for the capture or modeling of data. The newly ratified Darwin Core terms will support mobilization of data for GEO BON’s Essential Biodiversity Variables (EBVs), in particular the ‘species populations’ class. EBVs function as an intermediate layer between ‘raw’ data and the indicators established by governments under the CBD, and may also support assessments carried out for IPBES.

Interested users can learn more about these efforts by reading this primer about Publishing sample-based data with the IPT and by testing a prototype installation of the IPT v2.3 that supports sample-based datasets. Upon completion of testing, GBIF.org will begin supporting basic registration and search of sample-based data sets, with enhanced indexing and discovery of datasets expected during the second half of 2015.


Photo of a biologist holding up a common musk turtle during a survey of basking turtles. By Florida Fish and Wildlife, Karen Parker. CC BY-ND 2.0

New GBIF task force to speed up access to natural history collection data

Publicerat av GBIF.org --


A team of international experts convened by GBIF intends to help accelerate the discovery of and access to information about the world’s undigitized specimen collections.

The task force on accelerating the discovery of bio-collections data will start by defining the essential information needed about various types of collections. This ‘metadata’ will describe the contents of each collection and help data holders to assess and prioritize their digitization activities.

“The world’s natural history collections are estimated to contain between 2.5 and 3 billion specimens, and at least 90 per cent of them are undigitized”, said Siro Masinde, programme officer for content mobilization at the GBIF Secretariat. “While these collections offer vast untapped sources of species information, their sheer scale represents a huge challenge in terms of digitization efforts. By improving and increasing access to metadata that effectively describe collections’ contents, institutions can set better priorities more quickly and make persuasive business cases for digitization.”

The task force, comprised of members from the United States, Brazil, the United Kingdom, Benin, France and Japan, will develop a strategy and an action plan through consultations with experts from other institutions, digitization initiatives and projects as well as potential funders. It also expects to share guidance on mobilizing metadata while documenting successful business models.

The task force is chaired by Leonard Krishtalka from the Biodiversity Institute at the University of Kansas. The other members of the group are,
•    Barbara Thiers, New York Botanical Garden (United States)
•    Deborah Paul, iDigBio, Florida State University (United States)
•    Eduardo Dalcin, Jardim Botânico do Rio de Janeiro (Brazil)
•    Ian Owens, Natural History Museum, London (United Kingdom)
•    Jean Ganglo, University of Abomey-Calavi (Benin)
•    Marc Pignal, Muséum National d'Histoire Naturelle (France)
•    Masanori Nakae, National Museum of Nature and Science (Japan)


Stockholm Phylogenomics Group – Talk at NRM 24 March: SUPERSMART. Change in time!

Publicerat av Johan Nylander --

Dear All!

Reminder and change of starting time!

Stockholm Phylogenomics Group announces – Upcoming talk at the Naturhistoriska riksmuseet, Stockholm, March 24.

Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
the Netherlands)

Title: SUPERSMART: Ecology and evolution in the era of big data

Time: March 24 at 15:30-16:30

Venue: Room 525, Naturhistoriska riksmuseet, Stockholm

Host: Fredrik Ronquist

Abstract: Rapidly growing biological data volumes – including
molecular sequences and fossil records – hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see


Swiss non-profit Plazi becomes a GBIF Participant

Publicerat av GBIF.org --


Plazi, a Bern-based non-profit organization that supports and promotes linked open-access biodiversity data from digital taxonomic literature, has formally joined the GBIF network as a non-country Participant.

Building on the strength of partnership that has already seen Plazi publish more than 1,100 datasets, this step enables them to endorse publishers that wish to share their data through GBIF.org. 

Plazi maintains the Taxon Search Portal, a searchable digital taxonomic literature repository. In March 2014, the organization helped create a new workflow that provides immediate and open access to data underlying discovery of new species and shares it through EOL, Biodiversity Data Journal and GBIF.org. Publishers like Plazi and Pensoft are leading the conversion of traditionally published articles into digital formats that connect peer-reviewed research with the data that make it possible, simultaneously preserving and disseminating it more widely.

“By formally joining GBIF, Plazi advances the shared efforts of both organizations to provide critically needed access to vast stores of data and knowledge about species found in biodiversity literature,” said Donat Agosti, president of Plazi. “We are hastening a new kind of journal publishing that builds bridges between traditional scientific literature and the kind of records often mobilized by the GBIF network.”

Plazi becomes the 39th non-country Participant and the 94th member overall in the GBIF network.