Philosophical Transactions of the Royal Society B (2014) doi: 10.1098/rstb.2013.0190

Assessing and predicting ecosystem responses to global environmental change and its impacts on human well-being are high priority targets for the scientific community. The potential for synergies between remote sensing science and ecology, especially satellite remote sensing and conservation biology, has been highlighted by many in the past. Yet, the two research communities have only recently begun to coordinate their agendas. Such synchronization is the key to improving the potential for satellite data effectively to support future environmental management decision-making processes. With this themed issue, we aim to illustrate how integrating remote sensing into ecological research promotes a better understanding of the mechanisms shaping current changes in biodiversity patterns and improves conservation efforts. Added benefits include fostering innovation, generating new research directions in both disciplines and the development of new satellite remote sensing products.

Europe's brown bear, wolf, wolverine, lynx – at least one of these species can now be found in 21 EU Member States. After a lengthy period of decline their numbers are growing once more, but coexistence with man can be problematic. In an effort to solve the social and economic problems that sometimes result from this new expansion, the European Commission has launched a platform where farmers, conservationists, hunters, landowners and scientists can exchange ideas and best practices on sharing the same land with large carnivores.

The EU Platform on Coexistence between People and Large Carnivores will support constructive dialogue between key stakeholder organisations at the European level. Launching the platform, EU Environment Commissioner Janez Potočnik said: "We need to treat our natural neighbours with respect – but we also need to heed the concerns of those whose lives are genuinely affected by their close proximity. My warm congratulations to the organisations that have worked together to set up this important platform, which represents a major step forward in efforts to address the issue of peaceful coexistence."

The European Union is home to five species of large carnivores. All suffered dramatic declines in numbers and distribution as a consequence of human activity, but increasing protection and public awareness about their vital role in healthy ecosystems have caused many populations to stabilize or increase, and to return to areas from which they had been absent for decades or even centuries.

While this recovery is seen by some as a great conservation success, it has not been without its opponents. The issue involves a diversity of stakeholders such as hunters, foresters, livestock producers, reindeer herders, landowners, rural communities, conservation organizations and the wider public. These groups are influenced by and perceive large carnivores in different ways, and in some cases these differences can be a source of conflict. The platform will facilitate exchanges of knowledge and promote ways and means to minimize, and wherever possible, find equitable solutions to these conflicts.

The platform launched today follows a number of efforts to understand the conflicts between stakeholders over large carnivores, the results of which were set out in workshops conclusions and in a report.

Next steps

The Platform will hold its first working session immediately following the official launch today, on 10 June. It will adopt terms of reference and a work plan. The Platform will hold one annual meeting and organize additional workshops on selected topics. It will be supported by a web-based resource centre that will serve as the main tool to disseminate information on the activities of the platform, identify good practices in the form of documents or a manual, act as a gateway to the portals of the member organisations, and host media resources such as press kits for journalists.

For more information:

Original press release: http://europa.eu/rapid/press-release_IP-14-648_en.htm

Visit the large carnivore website of DG Environment at http://ec.europa.eu/environment/nature/conservation/species/carnivores/index_en.htm

http://ec.europa.eu/environment/nature/index_en.htm

The signing ceremony and moderated panel discussion is streamed (https://new.livestream.com/corlive1/events/2977474/embed) on the internet (also see http://ec.europa.eu/environment/nature/conservation/species/carnivores/index_en.htm)

Target group: programmers, developers and system engineers. The workshop is open to anybody who might be interested to learn more about the DINA-system.

Preliminary agenda:

• Presentations from all DINA-partners
• APIs, service oriented architecture and road map for distributed development, guidelines and principles on how to build a module and join the DINA-system
• Case studies
• Delivery options: creating installations from hosted environment, virtual machines down to code.

A detailed program will be available by the end of August 2014.

There will be a SETF-meeting for DINA consortium members on the 15th of September.

Welcome to register for the workshop here:

DINA - Technical Workshop 16-18 September, Stockholm

The workshop is an activity within WP 1 Task 1.4

The June 2014 updates of FishBase and SeaLifeBase are now available online!

FishBase: www.fishbase.us; www.fishbase.ca

FishBase stats to date: 32800 Species, 303100 Common names, 53900 Pictures,
50200 References, 2110 Collaborators, 700000 Visits/Month

SeaLifeBase: www.sealifebase.ca

The classical treatise "Flora of Northumberland and Durham" by Nathaniel John Winch is re-published through the innovative Advanced Books platform as an example of combining modern information technology together with historical scholarship to create a new sort of resource and data re-use. This publication will be supporting ongoing research on the botany of the region, which can be seen as a model for other regions in Europe.

The on-line semantically enriched re-publication marries the meticulous detail of old books with the interconnectedness of the internet bringing advantages of the digitization and markup efforts such as data extraction and collation, distribution and re-use of content, archiving of different data elements in relevant repositories and so on.

"Historic biodiversity literature is not just of cultural interest, it can be used to chart biogeographic change and help us understand the impacts of environmental change on biodiversity. Even if we are trying to predict future scenarios for biodiversity, understanding the changes of the past will help understand the changes we should expect in the future" said Dr Quentin Groom from the Meise Botanical Garden, Belgium, who initiated the project and marked up the original text.

The North-east of England has seen many changes since the publication of Winch's Flora. In the 19th Century the area was a powerhouse of the industrial revolution. It was an important coal mining area and significant for the production of iron and steel. It was also a centre for industries such as shipbuilding and engineering. In contrast the uplands in the west of the region were some of the most isolated areas in England, covered in blanket bog and rarely visited.

Since that time heavy industry and mining have declined, but the population has continued to grow. Agriculture and forestry have become mechanized changing the countryside perhaps beyond the recognition of Winch. Many of the plants and localities he mentions have disappeared and a large number of new species have been introduced. The local botanists are still very active in the region. With GPS systems and modern maps they are mapping the region's flora in ever more detail.

The extensive efforts of Quentin Groom from the Botanic Garden Meise and editor of this re-publication combined with the cutting-edge technologies for semantic enhancements used by Pensoft's Advanced Books platform, have resulted in additional details including links to the original citations and coordinates of the mentioned localities. In some cases the habitat that Winch described for a locality differs dramatically from what can be found in the same location nowadays.

The flora, for example, frequently mentions Prestwick Carr, an area of lowland bog, once full of rare species. Sadly it was largely drained just thirty years after the publication of the flora. Yet in recent years the Northumberland Wildlife Trust has been working to restore the bog to its former glory. "When reading Winch's flora, it is easy to see what has been lost, but more importantly what remains to be conserved", comments Groom.

The re-publication of Winch's flora is just one step towards fully understanding all the impacts on wild plants of all the environmental changes that have occurred since the 19th century. Nevertheless, digitization of this flora not only tells us about plants but also about the history of science. Between the lines of this flora one can see a rudimentary understanding of ecology and the beginnings of research on phytogeography.

Consider that in 1831 Charles Darwin set sail on the Beagle, collecting and cataloguing biodiversity around the world, much as Winch had done in North-east England over the preceding 30 years. Field botany at the time was not just a hobby, but a serious pursuit that led to many new discoveries.

Understanding the causes of biodiversity change is only possible if you have data over a long period. The North-east England has an enviable botanical history dating back to William Turner (1508-1568), the so-called, Father of English Botany, who came from Morpeth in Northumberland. Yet he was only the first in a long list of North-eastern botanists, including John Wallis (1714-1793), Nathaniel John Winch (1769-1838), John Gilbert Baker (1834-1920), George Ralph Tate (1805-1871), Gordon Graham and George Swan (1917). Their publications and the works of many others have contributed to a large corpus of literature on the region's flora.

Full article available at: http://dx.doi.org/10.1186/1471-2105-12-S15-S1 

An innovative workflow reveals new research potential of the Barcode of Life Data Systems (BOLD). A recently published article in the Biodiversity Data Journal (BDJ) used specimen records downloaded from BOLD in tabular format and imported these into a human-readable text developed in manuscript within the Pensoft Writting Tool (PWT). Data were used to study the species distributions of ten Nearctic species of braconid wasps from the Microgastrinae subfamily.

BOLD is originally designed to support the generation and application of DNA barcode data. However, the repository also holds unexplored treasures of additional data that provide unique potential for many other research uses.

Currently almost 4 million sequences (over 3.4 million of them DNA barcodes) are stored in BOLD, including coverage for more than 143K animal species, 53K plant species, and 16K fungi and other species, and this impressive storage of information is continuing to grow every day.

A team of researchers, led by Dr Jose Fernandez-Triana from the University of Guelph, Canada, have now explored how the unique amount of data stored on the BOLD platform can be utilised for new research purposes. Choosing tiny parasitic wasps for their case study they selected a sample of 630 specimens and 10 North American species. Data stored on BOLD were then used to uncover a significant number of new records of locality, provinces, territories and states.

The research was then secured a fast publication via BDJ, a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind.

"Import of structured data into human-readable text is important but it does not represent the whole story. More importantly, the data can be downloaded straight from the article text by anyone for further re-use, or be automatically exported to data aggregators, such as the Global Biodiversity Information Facility (GBIF). In this way, data platforms could get more peer-reviewed content from scholarly publications and scientists will be properly credited for their efforts" said Prof. Lyubomir Penev, founder of Pensoft Publishers.

Original Source:

Fernandez-Triana J, Penev L, Ratnasingham S, Smith M, Sones J, Telfer A, deWaard J, Hebert P (2014) Streamlining the use of BOLD specimen data to record species distributions: a case study with ten Nearctic species of Microgastrinae (Hymenoptera: Braconidae). Biodiversity Data Journal 2: e4153. doi: 10.3897/BDJ.2.e4153

Additional information:

The workflow is part of the Data Publishing Toolkit elaborated within the EU FP7 funded project EU BON (Grant agreement No 308454).

High-quality biodiversity data is essential for answering key questions on biodiversity in Europe, for example regarding the state and trends of species or for evaluating ecosystem services and functions on various scales. A new EU BON report "Gap analysis and priorities for filling identified gaps in data coverage and quality" evaluates the state of available biodiversity information and points out gaps of available biodiversity information sources.

The report aims to assess relevant data sources on biodiversity on a European and global scale. The assessment particularly evaluates the gaps of available biodiversity information sources and, after outlining the most important ones, identifies priorities for improving the data availability and gives recommendations of how they can be closed.

The report is divided into three main sections, starting first with an overall overview of gaps and limitations of biodiversity datasets. After outlining some general limitations of biodiversity data in Europe, the key findings from the specific analyses are summarized along with recommendations of how existing gaps can be closed. The last part presents a chapter containing the specific gap analysis for a selection of several main global and European datasets. The datasets represent some main sources for biodiversity data, either for specific realms (terrestrial, marine, freshwater), taxonomic groups, thematic fields (taxonomy, genetic databases) or networks of European test sites.

A new report "A world that counts - Mobilising the Data Revolution for Sustainable Development" was recently published. The document points out the need for globally available and freely accessible data to monitor progress of Sustainable Development Goals (SDGs), to hold governments accountable and foster sustainable development. This issue needs to be solved in a timely manner, as the gaps between developed and developing countries, between information-rich and information-poor people are increasing. Furthermore, better integrated, timely and validated information can lead to better decision-making and real-time feedback to the citizens. However, still some challenges remain, and the report points out recommendations to overcome existing limitations (countries have poor data, data arrives too late, many issues are barely covered), e.g. through a global "Network of Data Innovation Networks" that connects both organizations and experts. 

The report was written by UN-IAEG, which is the United Nations Secretary-General’s Independent Expert Advisory Group on a Data Revolution for Sustainable Development and is available online here: http://www.undatarevolution.org/wp-content/uploads/2014/11/A-World-That-Counts.pdf

The Mediterranean Institute for Biodiversity and Ecology (IMBE, Aix-Marseille University, Aix-en-Provence, France), in its research group "Macroecology and Biogeography of Global Change (MacroBio)" has a PostDoc position open for applications. The post has a duration of 36 months, the initial contract is made for 18 months, being extended based on an assessment of performance. The position is funded by the European Commission through the FP7 Research Project LUC4C and affiliated to the French National Scientific Research Centre (CNRS).

The main topic is to improve the way LULCC processes are represented in the DGVM LPJmL through enhanced soil and vegetation process representation. Work should improve the model's capacity to project climate-LULCC interactions for the computation of net climate effects, and ecosystem services. One focus is on the representation of diverse agricultural management systems, cropland abandonment/afforestation and forest management, in order to develop ways to account for their effects on biochemical cycles and biophysics.

The second EU BON Roundtable took place on 27 November 2014 at the Museum für Naturkunde in Berlin. The workshop was dedicated to explore ways in which EU BON can support citizen science (CS) activities. EU BON is building a large integrated biodiversity information infrastructure in order to serve science, policy and administration as well as citizen scientists. Citizen scientists are important stakeholders, as they support the increase of knowledge in various aspects, they may debate research questions, most often they collect data, and they may interpret data and publish their results.

Many partners and interested stakeholders participated, coming from different European research institutions, Natural History Museums, SMEs or representatives from European Institutions like European Commission DG Research & Innovation, the European Environmental Agency or the JRC and EU-funded Citizen Science projects.

Participants at the 2nd EU BON Stakeholder Roundtable

The Citizen Science Roundtable started with a "Setting the scene" session where a welcome address was given by Katrin Vohland from the Museum für Naturkunde (MfN). In a brief introduction from a biodiversity data perspective, some gaps in current bio-diversity data were shown, for example the large data gaps in Eastern European data in plant datasets and the restricted access to many datasets. Christoph Häuser from the MfN outlined EU BON and its main activities in the field of Citizen Science.

As a representative from DG Research and Innovation from the European Commission, Jose-Miguel Rubio-Iglesias showed the possibilities of Citizen Science as one option to improve the science-society bridge. Lucy Robinson (ECSA/NHM London) focused on citizen science in Europe, its impact and development. 

The next session targeted the question of how EU BON can possibly support data mobilization of and for citizen scientists. Antonio García Camacho from CSIC Donana showed, with a colleague from IBM, the prototype of the future EU BON data portal, to integrate biodiversity data/metadata sources into a single user interface. In another talk, Jaume Piera pointed out the requirements that exist in a CS portal, e.g. with regards to the role of citizen collaboration, the social media channels, and particularly the conceptual requirements. Important aspects here are for example that data access tracking has to be guaranteed, for giving credits to data producers and for keeping track of data use. Simao Belchior of the SME Simbiotica showed successful ways of visualizing georeferenced data, e.g. the mapping of pan-tropical forest clearing.

The next session called "A spotlight on some (meta)data provider" was started by Veljo Runnel who presented an assessment of Citizen Science involvement in biological research. Nils Valland described in his talk key success factors for citizen science and species occurrence data in Europe. Dirk Schmeller informed the audience about Volunteer Species Monitoring in Europe. He pointed out the need that governments should invest more to support and expand current monitoring initiatives. For example the EuMon project had documented 395 monitoring schemes for species, which represents a total annual cost of about €4 million, involving more than 46,000 persons devoting over 148,000 person-days/year to biodiversity monitoring activities.

In the "Synergies of European Citizen Science projects" session, presentations outlined of the main aims of several EU funded Citizen science projects (Citclops, COBWEB, Socientize). Pierre-Philippe Mathieu from the European Space Agency highlighted the new era for Earth Observation and links to Citizen Science projects. Siro Masinde from showed the Citizen Science activities of GBIF, which is one of the largest data providers of species occurrence records.

For more detailed information on the issues discussed, please see below the presentations from the meeting or contact us:

Dr. Katrin Vohland ( katrin.vohland@mfn-berlin.de)  

Dr. Florian Wetzel (florian.wetzel@mfn-berlin.de)

PRESENTATIONS

1.Rubio-Iglesias - Citizen Science as science-society bridge

2. Häuser - EU BON

3. Robinson - Citizen science in Europe

4. Camacho - EU BON biodiversity portal

5. Piera - Requirements for the EU BON biodiversity

6. Belchior - Fall of data portals and future of data workflows

7. Runnel - Assessing Citizen Schience involvement

8.  Arvanitidis - Crowdsourcing initiatives in the Mediterranean Basin

9.  Valland - Key success factors of citizen science

10. Schmeller - Volunteer Species Monitoring

11. Mathieu - Crowd Sourcing for Space Science

12. Sanz – Socientize

13. Ceccaroni – Citclops

14. Williams – COBWEB

15. Masinde - GBIF, plans for integrating Citizen Science data

Meeting agenda

Selection of pictures from the meeting:

A second WP4 (Link environment to biodiversity: analyses of patterns, processes and trends) meeting was held on 8 & 9 December 2014 in Brussels, to discuss progress towards objectives and set plans for future development.

Hot topics during the meeting were: GBIF data: who will use them, and how; development and use of methodology; collaboration between WP4 and the relevant WP3 (Improving tools and methods for data analysis and interface) and WP5 (EU BON testing and validation of concepts, tools, and services); as well ways to translate WP4 results for the use of policy and practice.

Image: Participants at the meeting;  Credit: Dirk Schmeller

FishBase on the US and CA servers (www.fishbase.us and www.fishbase.us) are now updated to version February 2015.

The domain www.sealifebase.org is now served with load balancing between the two mirrors below.

- sealifebase.ca (UBC, Vancouver)
- sealifebase.de (Geomar, Kiel)

You will see which mirror is serving at the bottom left corner of the page.

The DE domain is recently acquired.

New research published with the support of the FP7 large-scale bioinformatics project Building the European Biodiversity Observation Network (EU BON) and the Alien Challenge COST action reveals the importance of open data in the study and control of invasive alien species. The study was published online in open access in the journal Management of Biological Invasions.

Invasive alien species cause a wide variety of problems, including issues related to conservation; to human and animal health; to agriculture and to fisheries management. But how can science be useful to manage such potential issues?

"To advise policy makers and inform land managers on the dangers posed by and how to fight alien species we need to understand the invasion process. Ideally, we would like to be able to predict the causes, routes and progression of invasions." explains Dr. Quentin Groom, Botanic Garden Meise, Belgium.

Recently, several research groups have pioneered the process of "Horizon Scanning" for new alien species, also there have been parallel developments in the creation of dynamic ecological models to predict invasions. However, the greatest limitation to these advances is the lack of suitable data.

"The problem of invasive species is international and rapidly changing. Data are required from an extensive area, for many species and for a long period but what is currently available is patchy and often inaccessible. We argue for the importance of open data to tackle the problem of invasive alien species." explains Dr. Groom.

This new research reviews why access to data are so important to invasive alien species research and gives an overview of the reasons why data are unavailable to researchers. Currently access to data is patchy and is restricted in many ways:

• Legally, the use of restrictive data licensing blocks its use.
• Technically, many software systems don't adequately support sharing, particularly in their provision of unique identifiers.
• Culturally, data secrecy is the default position for most organizations.

Currently invasive species data is patchy and often restricted legally, through the use of restrictive data licensing. Credit: Peter Desmet

Gradually, data are becoming more accessible and attitudes towards data access are changing. The advent of data publications allows researchers to attract citations from their data, while simultaneously making their data accessible and discoverable.

The community of biodiversity observers is highly fragmented and the creation of a European biodiversity network will improve communication so that grassroots biodiversity surveyors will understand issues of data sharing, citation and licensing that are so critical for a rapid response to invasive species.

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Original Source:

Groom QJ, Desmet P, Vanderhoeven S & Adriaens T (2015) The importance of open data for invasive alien species research, policy and management. Management of Biological Invasions 6: in press. doi: 10.3391/mbi.2015.6.2.02

EU BON and CETAF informatics groups had an astronomically successful meeting at Digitarium in Joensuu, Finland, 17-20 March 2015. The event coincided with solar eclipse and show of the decade for northern lights.

Major progress in data standards for information exchange took place during the week when the Biodiversity Information Standards TDWG organisation announced ratification of five new terms for quantitative biodiversity data, which had been proposed by the EU BON project one year earlier. The new terms include, in particular, organismQuantity and sampleSizeValue. This allows for exchange of ecological data in much wider scale than what has been possible until now. The participants of the meeting applauded for this occasion.

Northern lights over Joensuu Science Park 2015-03-18. Photo: Riitta Tegelberg

The meeting included a training workshop on new data sharing tools, and working sessions for designing the EU BON portal, which will allow using biodiversity observation data in research.

The 40 attendees came from 18 different countries.

Participants at the meeting.

During the meeting the attendees also were given presentations and demonstrations of Digitarium's equipment and methods for high-performance digitisation.

Reporting under policy instruments to inform on the trends in biodiversity requires information from a range of different elements of biodiversity, from genetically viable populations to the structure of ecosystems. A new research looks into the Essential Biodiversity Variables as an analytic framework to identify ways in which gaps between biodiversity data and policy reporting needs could be bridged. The study was published in theJournal of Applied Ecology.

The Essential Biodiversity Variables (EBVs, Pereira et al. 2013) which were previously developed by ecology experts in GEO BON, is as a list of the most essential elements that need to be monitored worldwide, if we want to know how biodiversity is really changing.Example of essential variables is the population abundances of species (like the Living Plant Index from the WWF) or the extent of habitat fragmentation.

In the recently published study, funded by the EU FP7 project EU BON, scientists used the identified EBVs as a framework to analyse the gaps between the biodiversity objectives stated in international policy instruments, the indicators used to develop the related policy reports and the data that is actually available to quantify indicators and proxies.

Results of the recently published study show:

1) which aspects of biodiversity are being asked for the reporting on policy instruments. Based on this knowledge,it became apparent which aspects of biodiversity are not often asked to be in these reports and thus for which aspects policy makers are unlikely to receive information. For example information on the changes in the EBV class "Genetic Composition", was not often asked in reports, not often used in indicators and little data is directly available.

2) which of these biodiversity aspects actually end up being in the CBD reports, because scientists were able to quantify indicators. For instance, information for Ecosystem function is often asked for, but is not represented by many indicators.

3) for some EBVs data seems available to improve current reporting efforts, for instance for indicators on Ecosystem structure.

Additionally, the study identified which potentially available data could be used to improve existing indicators by adding more taxa or spatial or temporal coverage. This analysis also showed that the EBVs will not cover all the information asked in policy reporting. This is because the policy objectives also include things related to awareness raising of the public and the implementation of protection measures - aspects which are not within the scope of EBVs.

"Analytical properties, such as an identification of which data and indicators are relevant per EBV, will need to be addressed before EBVs can actually become operational and facilitate the integration of data flows for monitoring and reporting." commented the lead author of the study Dr. Ilse Geijzendorffer.

###

Original Source:

Geijzendorffer, I.R., Regan, E.C., Pereira, H. M., Brotons, L., Brummitt, N., Gavish, Y., Haase, P., Martin, C.S., Mihoub, J.-B., Secades, C., Schmeller, D.S., Stoll, S., Wetzel, F. T., & Walters, M.,Journal of Applied Ecology http://onlinelibrary.wiley.com/doi/10.1111/1365-2664.12417/abstract

Additional information:

Pereira, H.M., Ferrier, S., Walters, M., Geller, G.N., Jongman, R.H.G., Scholes, R.J. M. W. Bruford, Brummitt, N. , Butchart, S.H.M., Cardoso, A.C., Coops, N.C., Dulloo, E., Faith, D.P., Freyhof, J., Gregory, R.D., Heip, C., Höft, R., Hurtt, G., Jetz, W., Karp, D.S., McGeoch, M.A., Obura, D., Onoda, Y., Pettorelli, N., Reyers, B., Sayre, R., Scharlemann, J. P. W., Stuart, S.N., Turak, E., Walpole, M., & Wegmann, M. (2013) Essential biodiversity variables. Science, 339, 277-278.

XML markup of taxonomic research and specimen data is a valuable tool for structuring the incessantly accumulating biodiversity knowledge. It allows for the opportunity to collectively use the currently fragmented information for more detailed analysis.

A new research paper, published in theBiodiversity Data Journal, demonstrates how XML markup using GoldenGATE can address the challenges presented by unstructured legacy data, like those presented in the widely used PDF format. The paper demonstrates how structured primary biodiversity data can be extracted from such legacy sources and aggregated with and jointly queried with data from other Darwin Core-compatible sources, to present a visualization of these data that can communicate key information contained in biodiversity literature.

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals such as the Biodiversity Data Journal are using workflows that preserve the data's structure and semantic specificity and disseminate electronic content to aggregators and other users that makes these data reusable.

Such structure however is lost in traditional taxonomic publishing and currently, access to that resource is cumbersome, especially for non-specialist data consumers.

The question is: how do you manage this vast distributed repository of knowledge about biodiversity to make it easily available reusable for future research?

To answer this challenge this project queried XML structured articles published in Biodiversity Data Journal along with historical taxonomic literature marked up using GoldenGATE, and represents the results as a series of standard charts. XML structured documents are maintained by the Swiss NGO Plazi and are freely available online.

In such form, data associated with specimens becomes much more valuable as it can reveal key information about a particular species, and even about the scientists who investigate them. Charts indicate at a glance, for example, what time of year and elevation range a species is likely to be found at, useful information if you want to search for it in the field.

Our accumulated biodiversity knowledge includes an estimated 2-3 billion specimens in natural history collections and 500 million pages of printed text. These are the data we need to answer questions that are relevant to our world today, like setting conservation priorities and anticipating the effects of climate change on biodiversity and ecosystem functions that affect the lives of people.

"In short, we have half a billion pages worth of biodiversity knowledge and are just learning how to query it. The real power comes when data from many articles are combined, queried, and reused for new purposes. Potential applications span the scientific, policy, and public spheres. When we all have better access to the information that already exists in the global corpus of biodiversity literature, this helps us do a better job of exploring what we don't know and wisely applying what we do." explains the lead author Dr Jeremy Miller, Naturalis Biodiversity Center.

###

This project was supported by pro-iBiosphere and EU BON, two FP-7 (European Union Seventh Framework Programme, 2007-2013) grants (No 312848 and 308454).

Sustainable governance of our biological resources demands reliable scientific knowledge to be accessible and applicable to the needs of society. To achieve this, the EU BON project aims to develop a European Biodiversity Observation Network that facilitates open access to biodiversity data of relevance to environmental policy, and to develop innovative platforms for sharing and conveying this information through visually effective and policy-relevant media.

As part of this endeavour, EU BON partners FishBase Information and Research Group (FIN), the Museum für Naturkunde Berlin (MfN), and the UNEP World Conservation Monitoring Centre collaborated to produce an infographic titled ‘Climate Change & Biodiversity: What may happen to bony fishes in the North Sea?’. This infographic explains the economic and ecological importance of bony fishes in the context of the North Sea. It also visualises potential changes to species diversity and composition over time, using habitat suitability and climate change predictions. These changes have been projected to 2100 based on modelled environmental conditions under the Intergovernmental Panel on Climate Change’s A2 emissions scenarios. The projections have direct policy relevance to Aichi Biodiversity Target 10 of the Convention on Biological Diversity, which seeks to understand trends in climatic impacts on community composition in ecosystems, and to thereby minimize these impacts.

The infographic was published on the 1^st June 2015 on page 26 of The Parliament Magazine’s ‘Green Week’ edition (Issue 413), which is distributed to all members of European Parliament, the European Commission, Presidency Office, Party political groups, and various other EU institutions, with over 50,000 readers worldwide. 

Stakeholders from across Europe are coming together at Green Week to discuss biodiversity and ecosystem services in Europe. The European Environment Agency (EEA) will present its latest findings, recently published in its reports 'State of nature in the EU' and 'The European Environment – state and outlook 2015'. 

The European Environment Agency's recent assessments, including The European environment – state and outlook 2015 and State of Nature in the EU, show that Europe's biodiversity is still being eroded, despite significant local improvements. To halt the loss of biodiversity, stabilise and restore degraded ecosystems, the European Union has adopted the EU Biodiversity Strategy to 2020, which sets various targets and actions. An effective implementation of the strategy depends, among others, on the data and information available on biodiversity in Europe. Through its extensive network and close collaboration with partners, the EEA contributes extensively to the knowledge base on Europe's biodiversity.

Read the full original news story on the EEA website.

The 9th GEO European Projects Workshop is now taking place on 15 and 16 June 2015 in Copenhagen, co-organised by the Danish Meteorological Institute, the European Commission and the European Environment Agency.

While registration is now closed, due to demand the event will be recorded and streamed live on http://stream.dvc.dk/9thgeo/ for those who are interested to follow.

The objective of the GEO European Projects Workshop is to bring together European players interested in and actively contributing to the Global Earth Observations System of Systems (GEOSS). The aim is to enable participants to present their work and discuss how Europe can contribute to this international effort. Its timing has been set to maximise early insight and awareness of the new Implementation plan for the next decade of GEO as well as input to and awareness of Horizon 2020 work programme for 2016 and 2017.

Building on the experience from previous GEO European Projects Workshops, it is intended to continue working towards greater involvement of the European private sector, especially SMEs, in GEO.  The workshop will also focus on user engagement, and the priorities for future flagship initiatives, foreseen to be strengthened in the next phase of GEO, in order to fulfil GEO's ambition to provide information for decision making.

More information available on the official event page: http://geo.pbe.eionet.europa.eu/

The report ‘EU 2010 biodiversity baseline - adapted to the MAES typology (2015)’ presents a revised overview of the EEA's EU 2010 biodiversity baseline report.

The revision is necessary because the typology of ecosystems used in the 2010 report has since been altered by a working group of biodiversity experts. The revised report provides recalculated information on the state and trends of the different biodiversity and ecosystem components, based on the new typology of ecosystems.

Find the report here.

One of our recent associated partners, the EU project GLOBIS-B has published its first paper: "Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs)". You can find the article here.

Abstract: 

Essential biodiversity variables (EBVs) have been proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to identify a minimum set of essential measurements that are required for studying, monitoring and reporting biodiversity and ecosystem change. Despite the initial conceptualisation, however, the practical implementation of EBVs remains challenging. There is much discussion about the concept and implementation of EBVs: which variables are meaningful; which data are needed and available; at which spatial, temporal and topical scales can EBVs be calculated; and how sensitive are EBVs to variations in underlying data? To advance scientific progress in implementing EBVs we propose that both scientists and research infrastructure operators need to cooperate globally to serve and process the essential large datasets for calculating EBVs. We introduce GLOBIS-B (GLOBal Infrastructures for Supporting Biodiversity research), a global cooperation funded by the Horizon 2020 research and innovation framework programme of the European Commission. The main aim of GLOBIS-B is to bring together biodiversity scientists, global research infrastructure operators and legal interoperability experts to identify the research needs and infrastructure services underpinning the concept of EBVs. The project will facilitate the multi-lateral cooperation of biodiversity research infrastructures worldwide and identify the required primary data, analysis tools, methodologies and legal and technical bottlenecks to develop an agenda for research and infrastructure development to compute EBVs. This requires development of standards, protocols and workflows that are ‘self-documenting’ and openly shared to allow the discovery and analysis of data across large spatial extents and different temporal resolutions. The interoperability of existing biodiversity research infrastructures will be crucial for integrating the necessary biodiversity data to calculate EBVs, and to advance our ability to assess progress towards the Aichi targets for 2020 of the Convention on Biological Diversity (CBD).

Original Source:

W. Daniel Kissling et. al. (2015) Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs). Biodiversity. DOI: 10.1080/14888386.2015.1068709

We are happy to announce that earlier this summer EU BON has been selected to be featured as a successful EU-funded project. The DG Research & Innovation communication team has interviewed our project co-ordinator Christoph Häuser and the resulting article - Combining citizen and satellite biodiversity data - is now a fact!

The news item focuses on EU BON's efforts to bring together biodiversity and Earth observation data, that are accumulated from data sources ranging from the individual citizen scientist, researchers to the most technologically advanced satellites in one EU-wide initiative. 

"Information on life on Earth is crucial to addressing global and local challenges, from environmental pressures and societal needs, to ecology and biodiversity research questions," commented Christoph Häuser in his interview.

View the full story on the Horizon 2020 site.

The fifth EU BON Policy brief focuses on the need for open data in biodiversity monitoring. The Group on Earth Observation’s Biodiversity Observation Network, of which EU BON is a part, has a vision to better monitor and manage the global biosphere for our common good. This creates research challenges that require use of all appropriate data. Yet, access to data is impaired because, traditionally, few data are released, they are often locked up in traditional scientific literature, or because of concerns over intellectual property rights.

Because of this, EU BON endorses the free and open exchange of data and knowledge in accordance with the "Joint Declaration on Open Science for the 21st Century", especially in regard to scientific information produced in Europe as outlined by the European Commission.

Find out more in the Policy Brief below:

The 2016 European Space Agency Living Planet Symposiumwill be held in Prague, Czech Republic from 9-13 May 2016 and is organised with the support of the Ministry of Transport, Ministry of Environment and Ministry of Education, Youth and Sports of the Czech Republic. The event follows previous successful symposia held in Edinburgh (2013), Bergen (2010), Montreux (2007) and Salzburg (2004).

The first announcement has been now released, with a deadline for abstract submission on 16 October 2015.

All received abstracts will be reviewed by a Scientific Committee, notification of acceptance will be provided in early February 2016. Registration to attend the event (free of charge) will be opened in February 2016, after the publication of the preliminary programme.

The objectives of the ESA Living Planet Symposium are to:

• Present  the  progress  and  plans for the implementation of ESA Earth Observation strategy and the relevance of ESA's EO Programme to societal challenges, science and economy.
• Provide an international forum to scientists, researchers and users to present and share state of the art results based on ESA's Earth Observation and third-party mission data.
• Review the development of Earth Observation applications.
• Present the Copernicus space component and operational services.
• Report on ESA’s Exploitation Programmes (i.e. Climate Change Initiative, SEOM, DUE, VAE, STSE).
• Introduce the current and future planned Earth Observation missions.
• Outline ESA’s international cooperation in the field of Earth Observation.
• Provide dedicated thematic tutorials and demonstrations.

For more information, please visit: http://lps16.esa.int 

Looked down on with scepticism by many taxonomists, handling big data efficiently is a huge challenge that can only be met with thorough and multi-layered efforts from both scientists and technological developers. Projects like the Pan-European Species-directories Infrastructure (PESI), started in 2009, prove that harmonised taxonomic reference systems and high-quality data sets are possible through dynamic, expertly created and managed online tools. The methods, results and future prospects of PESI are available in the open access Biodiversity Data Journal.

With environmental changes occurring at an unprecedented rate around the world, biological communication needs to be left off the pace at no point. Phenomena such as species' migration, extinction, intrusion; ecosystem stability; decline of pollinators and pest invasion have to be monitored closely and identified momentarily. In order to do so, proper identification based on reliable and easily accessible data is crucial.

Therefore, the three key objectives of PESI include standardisation in taxonomic reference systems, enhancement of the quality and completeness of taxonomic data sets and creation of integrated access to taxonomic information. The five pillars of biological community networks, Zoology, Botany, Marine Biota, Mycology and Phycology, have been integrated in five infrastructural components: knowledge, consensus, standards, data and dissemination.

As a result, PESI did not only merge data from a range of sources and published a total of nearly 450,000 scientific names online. It also maintains networks of outstanding experts and national focal points, so that it makes sure that the taxonomic information, it relies on, is always at its finest, while simultaneously takes care about delivering persistent standards and easily accessible up-to-date biodiversity data.

PESI results will also feed as an essential part for the advancement of relevant EU projects, such as Building the European Biodiversity Observation Network (EU BON). In the EU BON project, the PESI Backbone will be advanced to satisfy the needs of the GEO BON / GEOSS system, also serving as a taxonomic backbone for the projected EU BON Biodiversity Portal.

Aiming at standardisation and integration of taxonomic data across platforms PESI also works in close collaboration with other relevant projects including GBIF, LifeWatch, the Catalogue of Life, the Encyclopedia of Life, the Global Names Architecture, GÉANT, ViBRANT, OpenUp!,BioVeL, iMarine , EU BON and BiodiversityKnowledge .

"Scientific names are key carriers of biodiversity information. Therefore, for the efficient exploring and integration of biodiversity data, the development of a functional taxonomic resolution system, including the establishment of a shared taxonomic standard (as a core component), is essential for all sorts of biodiversity assessments. PESI provides such an infrastructure for Europe, integrating the relevant technical (informatics) and social (knowledge & users) networks into a common work program, serving a wide community of biodiversity workers," says Dr. Yde de Jong, coordinator of the Pan-European Species-directories Infrastructure (PESI) project.

"The PESI Taxonomic Backbone serves as a taxonomic data standard resource, facilitating and optimising the integration and sharing of European biodiversity data, supporting a wide range of European services, major biodiversity programs and stakeholders on nature conservation and biodiversity management," conclude their results the scientists.

Original Source:

de Jong Y, et al. (2015) PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848.doi: 10.3897/BDJ.3.e5848

Additional Information:

The Pan-European Species-directories Infrastructure (PESI) provides standardised and authoritative taxonomic information by integrating and securing Europe's taxonomically authoritative species name registers and nomenclators (name databases) and associated expert(ise) networks that underpin the management of biodiversity in Europe. PESI kicked-off as an EC-FP7 project, running from 2009 to 2011.

PESI proceeded from the EC-FP6 Networks of Excellence EDIT, on developing a European Distributed Institute of Taxonomy, and MarBEF, on Marine Biodiversity and Ecosystem Functioning.

Building the European Biodiversity Observation Network (EU BON) is a European research project, financed by the 7th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

Data collection and analysis are at the core of modern research, and often take months or even years during which researchers remain uncredited for their contribution. A new plugin to a workflow previously developed by the Global Biodiversity Information Facility (GBIF) and Pensoft, and tested with datasets shared through GBIF and DataONE, now makes it possible to convert metadata into a manuscript for scholarly publications, with a click of a button.

Pensoft has currently implemented the feature for biodiversity, ecological and environmental data. Such records are either published through GBIF or deposited at DataONE, from where the associated metadata can be converted directly into data paper manuscripts within the ARPHA Writing Tool, where the authors may edit and finalize it in collaboration with co-authors and peers and submit it to the Biodiversity Data Journal (BDJ) with another click. Until now, the GBIF metadata have been exported into an RTF file. The new feature will be also part of future Pensoft projects, including the recently announced Research Ideas & Outcomes (RIO) Journaland the forthcoming Ecology and Sustainability Data Journal.

The concept of the data paper was introduced in the early 2000's by the Ecological Society of America in order to solve issues of handling big data and to make the metadata and the corresponding datasets discoverable and citable. It was then brought to the attention of the biodiversity community in 2011 as a result of a joint GBIF and Pensoft project and later implemented in the routine publishing process in all Pensoft journals.

Since then, Pensoft has been working with GBIF, and subsequently DataONE to automate the process of converting metadata into a human-readable data paper format. The novel workflow means that with only a couple of clicks, publishers of datasets on either GBIF, DataONE or any other portal storing metadata in the same format, may submit a manuscript for peer-review and open access citable publication in BDJ.

The process is simple, yet it brings a lot of benefits. Publishing data does not only mean a citable publication and, thus, credit to the authors and the repository itself, but it also provides the option to improve your work and collect opinion though peer-review. BDJ also shortens the distance between "narrative (text)" and "data" publishing.

"Metadata descriptions (e.g., data about the data) are of primary importance for data dissemination, sharing and re-use, as they give essential information on content, scope, purpose, fitness for use, authorship, usage rights, etc. to any potential user. Authoring detailed metadata in repositories can seem a tedious process, however DataONE users will now benefit from direct export of already created metadata into data paper manuscripts and have even better exposure of their work through discoverability mechanisms and scholarly citations," commented Dr Amber Budden, DataONE Director for Community Engagement and Outreach

"It is great to reap the fruits of a process that started back in 2010. The automated streamlining of biodiversity data between repositories and publisher is an elegant feature that makes publishing a data paper an easy and rewarding process to crown scientists data collection efforts and ensure its use and re-use," added Prof. Lyubomir Penev, Managing Director of Pensoft.

More detailed information on how data authors could use the workflow can be found on the Pensoft blog.

References:

Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics. 12(Suppl 15):S2. DOI: 10.1186/1471-2105-12-S15-S2

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4(Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.

The Royal Museum for Central Africa (RMCA) in Tervuren (Belgium) is part of the FishBase Consortium and responsible for the information on the fresh- and brackish water fishes of Africa in the FishBase database. Through an agreement with the Belgian Development Cooperation and as part of the FishBase program, the RMCA has five (5) grants available for a 3-month training program in the use of FishBase and the taxonomy of African fishes.

The training will have three subsets:

1. A detailed explanation of FishBase in all its aspects;
2. A training in the taxonomy of African fishes;
3. A case study based on data from FishBase or on taxa for which taxonomic problems have been encountered.

This course has been offered annually since 2005 and is held at the Royal Museum for Central Africa (Leuvensesteenweg 13, B-3080 Tervuren, Belgium). For more information and to apply for this three-month training grant, see: http://fishbase.africamuseum.be or www.fishbaseforafrica.org. Please note that for 2016, this course will be given in French only.

Questions? Contact Dimitri Geelhand de Merxem (dimitri.geelhand@africamuseum.be).

Substantial amount of documented occurrence records is awaiting publication stored in repositories and data indexing platforms, such as the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD Systems), or Integrated Digitized Biocollections (iDigBio). In order to streamline the authoring process, save taxonomists time, and provide a workflow for peer-review and quality checks, Pensoft has introduced an innovative feature that makes it possible to easily import occurrence records into a taxonomic manuscript.

Prior to this development, Pensoft's ARPHA Writing Tool (AWT) only used the "upload from Excel" approach for this workflow. Although this method significantly simplified the process of importing materials and is actively used by the authors, it still required one extra transposition step.

Now, we added a new even more user-friendly option. By simply specifying an identifier (ID) in the relevant box, the new import plugin allows for occurrence data, stored at GBIF, BOLD systems, or iDigBio, to be be directly inserted into the manuscript. It all happens in the user-friendly environment of the AWT, where the imported data can be then edited before submission to the Biodiversity Data Journal.

Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can be easily downloaded from the article text into structured data by anyone who needs the data for reuse after publication.

Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD and iDigBio.

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4(Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.

The 1st GLOBAQUA International Conference will be held on 11-12 January 2016 in Freising, Germany. The interdisciplinary conference will go under the motto "Managing The Effects Of Multiple Stressors On Aquatic Ecosystems Under Water Scarcity".

The conference will serve as a platform for exchange and discus­sion of innovative scientific findings and methods in aquatic ecosys­tems research. It will focus on novel methods of environmental monitor­ing and modeling of various scopes, scales and structural complexity to improve process understanding the interconnectivity and feedback mechanisms of climate (regional), land use (regional), economy, hydrol­ogy and hydraulics (catchment and river), water quality (river), biology and aquatic ecosystems (reach scale). Further, the conference builds the bridge to the scientific assessment of implications on policy and management.

The deadine for submitting an abstract for the conference has been now extended until 7 Nov 2015.

More information on the conference, registration, abstract submitting is available on the GLOBAQUA website.

Post-doctoral scientist position is open for the project "Towards an integrated prediction of Land & Sea Responses to global change in the Mediterranean Basin" (LaSeR-Med), which focusses on integrated socio-ecological modelling. The duration of the contract is initially one year, with a possible extension for a second year, depending on the initial results. The post-doc will be based within the Mediterranean Institute of marine and terrestrial Biodiversity and Ecology (IMBE) in Aix-en-Provence, France. The project is part of the Labex OT-Med (http://www.otmed.fr/).

Applicants should hold a doctoral degree in physics, chemistry, microbiology, geosciences, environmental sciences or a related field of science. They should be familiar with modelling biogeochemical interactions between ecosystems and capable to further develop existing numerical ecosystem models. Programming skills (C) and modelling experience are therefore mandatory. Knowledge of R and of Unix/Linux environment will be an advantage. The candidate should have good written and oral communication skills. For work, good skills in the English language will be essential.

The project:

Terrestrial and marine ecosystems are connected through groundwater, river discharge and nutrient outflows (especially N and P). River catchments in the Mediterranean are N-intensive regions, mostly due to intensive agriculture in the North and to crop N2 fixation or food & feed import in the South. The fraction of nutrient reaching the sea constitutes significant anthropogenic forcing of many marine biological processes. For simulating the dynamics of the first levels of the marine food web (from nutrients to jellyfishes), the ocean biogeochemical model, Eco3M-MED, used and developed by the Mediterranean Institute of Oceanography (MIO) within OT-Med, currently uses N and P measurements at river mouths, e.g. for the Rhône.

In order to estimate the impacts of global change on the functioning of marine ecosystems, the project aims at modeling the dependency of N and P outflows to the Mediterreanean sea toward land management. Land management is modelled as part of the agro-ecosystem model LPJmL (Bondeau et al., 2007), that has been especially adapted to the Mediterranean cropping systems (Fader et al., 2015). Among others, LPJmL simulates the daily carbon and water cycles, and the river discharges to the sea. Following existing approaches in the scientific literature, the post-doc will implement the nutrient N and P transfer in LPJmL, covering the net nutrient inputs to the river catchments by accounting for the processes occurring at the agro-ecosystem level (N2 biological fixation, fertilization, atmospheric deposition) and the net food and feed imports. Since only a minor fraction of the net nutrient inputs from Mediterranean basins reaches the sea, the retention along the nutrient cascade will have to be added to the LPJmL river routing scheme, similarly to the method used by the Riverstrahler model. Once the nutrient transfers have been introduced into LPJmL, simulations will be validated using current climate and land use forcing for comparisons with the existing observations from river outlets. Finally, future conditions will be assessed by using the model with scenarios of changing regional climate and land use / land management.

Your application:

Applications should contain a suitable motivation letter describing your anticipated role in the project, a CV, a list of scientific publications and the names of at least two scientists that can be contacted for references. They must be sent to Ms. Gabriela Boéri (gabriela.boeri@imbe.fr). Please prepare your application as a single file in pdf-format.

Questions about the project or the position can be directed to Dr. Alberte Bondeau (alberte.bondeau@imbe.fr). The position will be filled as soon as a suitable candidate has been found – work should start soon after that date. The salary and contract conditions will be determined according to standards set by Aix-Marseille University – questions in this regard can be directed to Sophie Pekar (pekar@otmed.fr).

October 2015 updates for both FishBase (www.fishbase.org) and SeaLifeBase (www.sealifebase.org) are now online!

From 9 to 11 November in Vienna, Austria the EU H2020 project Detecting changes in essential ecosystem and biodiversity properties – towards a Biosphere Atmosphere Change Index: BACI has organised a special workshop titled "Remote sensing applications related to land use/change" with the aim to facilitate co-design and co-production of knowledge with regard to innovative applications of remote sensing products.

EU BON project partner Duccio Rocchini was among the invited lecturers at the event. His talk titled "Like in a Rubik’s cube: Recomposing Biodiversity Information by Remote Sensing Data" introduced some experience from EU BON.

The overarching objective of BACI is to tap into the unrealized potential of existing and scheduled space-borne Earth observation data streams to detect changes in ecosystem functioning and services that have repercussions for essential biodiversity variables, land use potentials, and land-atmosphere interactions.

The 3rd EU BON stakeholder roundtable took place from 10 to 11 December 2015 in Granada, Spain. The meeting brought together participants from global, European and regional projects, institutions, governmental organizations and universities to discuss biodiversity data workflows across different scales. Other important issues to discuss were current limitations of workflows but also tools and products from EU BON and other projects that may help to improve data collection, analysis and use in policy and practice.

Images from the workshop showing participants and group discussions; Credit: Dirk Schmeller/Florian Wetzel

The roundtable focused on EU BON test sites, workflows of data/information and the further usage for policy reporting and political processes. These issues were discussed with partners from EU BON and related biodiversity projects (LTER, GEO BON, Life Watch, Ecoscope) and stakeholders of biodiversity data (regional biodiversity networks: the environmental information network of Andalusia (Rediam), the Center for Monitoring and Assessment of Global Change (CAESCG), the Life project ADAPTAMED as well as local scientists).

On the first day, the different approaches from global (GEO BON) and European projects (EU BON, LTER, Life Watch, Ecoscope) were presented with a special emphasis on data collection, integration and analysis tools from EU BON. Furthermore, regional stakeholders pointed out their demands with regards to data mobilizations issues.

During the second day, discussions focused on the workflow of biodiversity data and the current barriers was discussed and current barriers and possible solutions to overcome the problems. Currently particularly socio-economic data is lacking as well as funding schemes to support interdisciplinary work as well as lacking capacities to address these questions.

In the World Café session, smaller groups discussed details of the workflow, particularly on (1) data mobilization, (2) data and tools, (3) implementation, and (4) upscaling.

As outcomes of the discussions at the round table, several recommendations were drafted, for example, to prioritise developed EU BON tools for further usage in the project and through the portal, to better address the user groups on different levels and provide a detailed and specific description for the tools. There are several biodiversity data workflows existing at the test sites, that could be improved by additional / existing tools, guidelines and standards from projects such as EU BON and by an enhanced communication between local sites, regional networks (as "middle-ware") and European networks.

Overall, it was agreed that a showcase for the workflow of biodiversity data from collection up to visualization (e.g. maps and using user such as the Andalusian Rediam network or/and IPBES as an example) is needed to showcase better the benefits of a European biodiversity network and enhance current functionalities by analyzing barriers and limitations in such an example of an "EU BON storyline".

Presentations:

Presentations Day 1

Presentations Day 2

Picture: Main European networks, projects and regional participants; Credits: Dirk Schmeller/EU projects logos

Are you in Eastern Europe and actively involved in monitoring and managing biodiversity data? Then the EU BON "Biodiversity data sharing and data publishing workshop" might just be the thing for you.

The event will take place on 22-23 March 2016 in Sofia, Bulgaria with focus on publishing of biodiversity data, in particular species occurrences, sample-based and citizen science data. The training will include a practical session during which participants will be assisted by experienced trainers from the EU BON project. To register and for more information, click here.

The sessions on data sharing will cover introductory overview of key concepts, demonstration and practical exercise using the GBIF Integrated Publishing Toolkit (IPT). The Global Biodiversity Information Facility (GBIF) is the world's largest initiative for enabling free access to biodiversity data via internet.

Special attention will be paid to data paper publishing led by specialists from Pensoft Publishers - a company well known among biodiversity scientists worldwide for technologically cutting-edge open access journals, such as: Research Ideas and Outcomes, ZooKeys, Biodiversity Data Journal, Nature Conservation, and a strong advocate of data publishing. Registration of data in GEO registry system will be also addressed during the workshop.

The following topics will be covered (detailed program will follow):

• The data publishing landscape, gaps and mobilization efforts
• Demonstration and practical session on data publishing using the GBIF IPT: step-by-step demo will show in detail (and in practice) how to publish a dataset using IPT.
• The Data Publishing Toolkit at EU BON: Automated creation of data papers, data and text integrated publishing via the ARPHA Publishing Platform
• Citizen Science gateway and demo of PlutoF Citizen Science module
• GoldenGate Imagine tool and copyright issues
• Registration of data in the GEO Registry System

Context and background: 

Addressing global problems, such as biodiversity loss and impacts of climate change requires open access to data. This was concluded by world leaders at Johannesburg Summit in 2002 when they established the Group for Earth Observations (GEO). EU BON (Building the European Biodiversity Observation Network) seeks to enhance biodiversity data availability and integration, and is the European contribution to the GEO Biodiversity Observation Network.

All biodiversity databases need to be integrated in GEO. Therefore, EU BON undertakes capacity building of biodiversity communities (e.g. researchers, citizen scientists, non-governmental organisations) that are involved in collecting and disseminating biodiversity information, including monitoring initiatives.

To register and for more information, click here.

The Faculty of Geo-Information Science and Earth Observation (ITC) at the University of Twente has recently launched an investment programme to strengthen its international academic fields. For 11 pioneering-multidisciplinairy projects a PhD-position is made available, three of them already are filled in. The Department of Natural Resources (NRS) specialises in advanced spatial and temporal analysis and technique development for the environment as well as sustainable agriculture.

Job Description: 

For more information visit the official job offer.

One of the main outputs of EU BON will be the establishment of an European Biodiversity Portal based on data collected and compiled from a variety of sources including earth observations but also observations and monitoring data from (local) sites. One of the main points of this portal is to serve as a substantial building block of a global biodiversity portal planned by the Group of Earth Observations project GEO BON.

But how will this portal be useful to stakeholders on a more local level - for example for people involved in questions connected to biodiversity across European regions? What will be the real benefits of it for biodiversity monitoring and conservation? Just a couple of weeks after the Third EU BON Stakeholder Round Table in Granada, Spain, Mr Clint Alibrandi from REDIAM (Environment and Water Agency in Andalusia) gives us his views on these questions.

Picture:  Excursion to Sierra Nevada.; Credit: Katrin Vohland

Q: REDIAM shares a mission with EU BON in its attempt to collect, standardize and distribute available biodiversity data. What will be the expected benefits and challenges in the process of making this type of datasets available for society and environmental policy?

A: Among the responsibilities of the Regional Environmental Government of Andalusia are promoting Social Environmental Awareness, Managing a vast, diverse and very complex territory, Control and Mitigate any threats posed to the fragile ecosystems present in our region as well as all the responsibilities derived from the management and planning of the existing natural resources.

Considering these facts, it is necessary to be able to account for the best environmental information available. Since the early 80’s the Regional Environmental Government of Andalusia has been working on its Environmental Information System with the purpose of generating, compiling, standardizing and analyzing Environmental Information covering topics such as Climate, Water, Air Quality and Biodiversity by means of ICTs. This the REDIAM. The name comes from the Spanish Acronym "REd De Información AMbiental de Andalucía" which means the Environmental Information Network of Andalusia. It serves as a Unified Regional Environmental Information Registry.

From this effort, the information obtained by the REDIAM is made publicly available to be then employed in Decision Making processes and Management Planning on behalf of the Administrations, for Dissemination and Awareness as well as for Research purposes.

As such, it is of vital importance for the REDIAM to be able to account for updated and verifiable Information and Data Sources and this is what we consider to be the most important benefit on behalf of EU BON, as it will offer the possibility to have a higher level reference covering a larger perspective, allowing stakeholders, be it either from a local, regional or national level, to consult or work with data, tools and have reference to relevant policies concerning Biodiversity on the European scale in order to be able to better transpose them to a more local context.

Yet the greatest challenge we believe that EU BON might come to face is the fact that the different contexts that exist over the whole European territory make it very difficult to tailor tools and information formats which can cover the different priorities or needs that exist in the diverse makeup of stakeholders that exist from a local, regional and national perspective. The same can most probably apply to the feedback, queries or requests made to EU BON on behalf of the stakeholder and user community. It is never easy to reach a common base level and from the regional perspective, REDIAM has faced the same type of situations.

Q: What type of stakeholders do you hope to engage through your network - who is using your data and for what purposes?

A: The stakeholders which are currently engaged with the REDIAM consist in Universities, Research Centres, Public Bodies, Local Administrations, Private Companies just to name a few examples. There are over 150 organizations which are partners of the REDIAM, they provide relevant Environmental Information to the REDIAM and are responsible for updating the information.

And as can be expected,the information provided is as diverse as the makeup of stakeholders that are part of the REDIAM, with the following formats being made available: Cartography, Satellites Images, Databases, Reports, Statistics, Applications, Management Plans and Programmes, Orthophotos, Indicators, Studies.

Additionally the REDIAM offers the user community different alternatives in order to access the previously indicated information. The REDIAM Channel is a web portal with a Catalogue and Information Search System, OGC Services, Query and Viewer tools, Downloader. The user community is able to access its information and services. This community consists in Citizens, Universities, Public Administrations and Companies from the Public and Private Sector.

Q: Where do you see the cross section between REDIAM’s work and EU BON - what are the products from EU BON and other European projects that would be helpful for the work that you are doing?

A: The REDIAM has great interest in the following issues and we believe that EU BON would be up to the task of providing solutions and/or guidelines on how to be able to proceed to solve them:

• The elaboration of a common tool for the description and localization of species throughout the European Territory. This can prove a very useful service for Environmental Impact Assessments by providing a more complete view on different species distribution on determined area.
• Defining a standardized list of species which contains the taxonomically correct name for each one of them. EU BON could serve as a base reference to set guidelines for standardizing the taxonomical classification of species.
• Support and guidance in defining specific biodiversity indicators as proposed by EUROSTAT, a methodological and assessment guide of some sort.

Q: In your opinion what are the three greatest benefits of a European level biodiversity portal?

A: 1) Offering an opportunity of Standardizing and Harmonizing Biodiversity related information. We all speak the same "language" when referring to Biodiversity, but it is necessary that we all be able to follow the same "rules" as well. This is the first and most important pillar we believe that a European level Biodiversity portal can bring into play.

2) It would allow for and facilitate a widespread exchange of information amongst stakeholders throughout the whole European Territory.

3) And finally, it would allow a common analysis on a European level which would provide a general assessment on how different efforts and policies are effective, value which is the real status of Biodiversity and/or specific species independently from the limit of administrative or country borders.

About REDIAM:

The Environmental Information Network REDIAM has onboard experts from the Regional Ministry of Environment in Andalusia and its Water and Environmental Agency. With a team expertise ranging from local to regional and European level and from technical know-how to regional and thematic assessment, the main aim of the network is to integrate all spatially-referenced biodiversity data produced in Andalusia. Raw data are used to generate knowledge and improve its distribution, making it accessible and comprehensible for the general public.

Creating and maintaining a biodiversity data collection has been a much-needed worldwide exercise for years, yet there is no single standard on how to do this. This has led to a myriad of datasets often incompatible with each other. To make the most out of biodiversity data and to ensure that its use for environmental monitoring and conservation is both easy and legal, EU BON published recommendations that provide consistent Europe-wide Data Publishing Guidelines and Recommendations in the EU BON Biodiversity Portal.

The report "Data Policy Recommendations for Biodiversity Data. EU BON Project Report" featured in the Research Ideas & Outcomes (RIO) journal, is the first contribution in a pioneering comprehensive project outputs compilation taking advantage of RIO's unique option to publish collections of project results.

Lyubomir Penev presenting the EU BON collection in RIO at the project's biodiversity data sharing and data publishing workshop in Sofia; Credit: Pensoft

Biodiversity data and information provide important knowledge for many biological, geological, and environmental research disciplines. Additionally, they are crucial for the development of strong environmental policies and the management of natural resources. Information management systems can bring together a wealth of information and a legacy of over 260 years of biological observations which are now dispersed in a myriad of different documents, institutions, and locations.

EU BON aims to build a comprehensive "European Biodiversity Portal" that will incorporate currently scattered Europe-wide biodiversity data, while at the same time helping to realize a substantial part of the worldwide Group on Earth Observations Biodiversity Observation Network (GEO BON). To achieve this ambitious plan, EU BON identifies the strong need for a coherent and consistent data policy in Europe to increase interoperability of data and make its re-use both easy and legal.

"Biodiversity data and information should not be treated as commercial goods, but as a common resource for the whole human society. The EU BON data sharing agreement is an important step in this direction," comments the lead author of the report Dr. Willi Egloff from Plazi, Switzerland.

In its report, the EU BON project analysis available single recommendations and guidelines on different topics. On this basis, the report provides structured guidelines for legislators, researchers, data aggregators, funding agencies and publishers to be taken into consideration towards providing standardized, easy-to-find, re-shareable and re-usable biodiversity data.

"We are extremely happy that EU BON is among the first to take advantage of our project outputs collections option in RIO. The first report they are publishing with us deals with issues of opening up data, and digitizing and collecting scientific knowledge, all close to RIO's mission to open up the research process and promote open science," says Prof. Lyubomir Penev, Founder and Publisher of RIO.

Original Source:

Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L (2016) Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes2: e8458. doi: 10.3897/rio.2.e8458

Engagement with relevant political authorities and other stakeholders is of crucial importance for a research project, making sure its objectives are in tune with the real-world problems and its results provide adapted solutions. Now EU BON shares the outcomes, lessons learned and conclusions from a series of three roundtable meetings designed to identify stakeholder needs and promote collaboration between science and policy.

The collection of EU BON stakeholder roundtable reports provides a summarized overview of shared experiences gained in the three different workshops that were organized from 2013-2016. With more than 100 participants from over 20 countries altogether, the roundtable reports provide insights and exchange of ideas on highly relevant issues concerning policy, citizen science and local/regional stakeholders and its networks.

Simplified workflow from data mobilization via processing to stakeholders from the practice; Credit: Vohland et al.

The roundtables seek to build up a stakeholder dialogue with exemplary sector-specific user communities to incorporate feedback loops for the products of EU BON, as well as to develop improvements of existing biodiversity data workflows. Being published via the innovative Research Ideas & Outcomes (RIO) journal conclusions, derived knowledge and results are now made available for other projects and the wider community to ensure their re-use.

The three roundtable papers report on conclusion on highly relevant issues related to biodiversity information and its open-access and availability, data workflows and integration of citizen science as well as science-policy interfaces.

"In each of the three detailed reports of the roundtables we outline its aims, intentions, as well as results and recommendations, that were drafted based on the roundtable discussions, world café sessions and working groups. Such project results are now published for the first time in the new series of EU BON results, featured in RIO, providing a unique new medium to share experiences, outcomes and conclusions," comments Dr. Katrin Vohland, Museum für Naturkunde, Berlin.

"The three reports were published as workshop report provided by the Research Ideas & Outcomes (RIO) journal. This allows readers to publish, distribute and computationally analyse myriads of workshop reports that otherwise often get forgotten or just lost," comments Prof. Lyubomir Penev, co-founder and publisher of RIO.

Original Sources:

Rationale of the roundtables

Wetzel F, Hoffmann A, Häuser C, Vohland K (2016) 1st EU BON Stakeholder Roundtable (Brussels, Belgium): Biodiversity and Requirements for Policy. Research Ideas and Outcomes 2: e8600. doi: 10.3897/rio.2.e8600

Vohland K, Häuser C, Regan E, Hoffmann A, Wetzel F (2016) 2nd EU BON Stakeholder Roundtable (Berlin, Germany): How can a European biodiversity network support citizen science? Research Ideas and Outcomes 2: e8616. doi: 10.3897/rio.2.e8616

Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. doi: 10.3897/rio.2.e8622

General synthesis and lessons learnt from the three EU BON stakeholder roundtables

The importance of measuring species diversity as an indicator of ecosystem health has been long recognized and it seems that satellite remote sensing (SRS) has proven to be one of the most cost-effective approaches to identify biodiversity hotspots and predict changes in species composition. What is the real potential of SRS and what are the pitfalls that need to be avoided to achieve the full potential of this method is the topic of a new research, published in the journal Remote Sensing in Ecology and Conservation.

The new study, supported by the FP7 funded EU project EU BON takes the assessment of diversity in plant communities as a case study. Showing the difficulties to achieve high results by relying only on field data, the paper discusses the advantages of SRS methods.

"In contrast to field-based methods, SRS allows for complete spatial coverages of the Earth's surface under study over a short period of time. Furthermore, it provides repeated measures, thus making it possible to study temporal changes in biodiversity," explains Dr. D. Rocchini from Fondazione Edmund Mach, lead author and WP deputy leader / task leader in EU BON. "In our research we provide a concise review of the potential of satellites to help track changes in plant species diversity, and provide, for the first time, an overview of the potential pitfalls associated with the misuse of satellite imagery to predict species diversity. "

Traditionally, assessment of biodiversity at local and regional scales relies on the one hand on local diversity, or the so called alpha-diversity, and on the other, on species turnover, or beta-diversity. Only in combination of these two measures can lead to an estimate of the whole diversity of an area.

While the assessment of alpha-diversity is relatively straightforward, calculation of beta-diversity could prove to be quite challenging. This is where increased collaboration between the remote sensing and biodiversity communities is needed in order to properly address future challenges and developments.

The new research shown the high potential of remote sensing in biodiversity studies while also identifying the challenges underpinning the development of this interdisciplinary field of research.

"Further sensitivity studies on environmental parameters derived from remote sensing for biodiversity mapping need to be undertaken to understand the pitfalls and impacts of different data collection processes and models. Such information, however, is crucial for a continuous global biodiversity analysis and an improved understanding of our current global challenges."concludes Dr. Rocchini.

Original Source:

Rocchini, D., Boyd, D. S., Féret, J.-B., Foody, G. M., He, K. S., Lausch, A., Nagendra, H., Wegmann, M., Pettorelli, N. (2016), Satellite remote sensing to monitor species diversity: potential and pitfalls. Remote Sensing in Ecology and Conservation, 2: 25-36. doi: 10.1002/rse2.9

A new EU BON acknowledging data article provides a virtual species set as a valuable tool in biodiversity monitoring. 

Abstract

Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700,000 random observations at the extent of Europe. The dataset includes spatial attributes such as: distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide-spread species.

Original Source:

Garzon-Lopez, C.X., Bastin, L., Foody, G.M., Rocchini, D. (2016). A virtual species set for robust and reproducible Species Distribution Modelling tests. Data in Brief, 7: 476-479. doi: http://dx.doi.org/10.1016/j.dib.2016.02.058

April proved to be an eventful month for EU BON, hosting the presentation of two major project results, not only within the same month, but in the course of one week. While CSIC and partners were launching the beta-version of the long-waited Biodiversity Portal in Seville, another EU BON team was busy to search for Integrated approaches for focused biodiversity data mobilization in Stockholm.

About the Portal:

In a dedicated session at the WP2 meeting in Seville, Spain, EU BON partners had the chance to view their work for the last couple of years materialising into one of the main expected project results - the European Biodiversity Portal. That said, what was then presented on 29 April is a beta version, with the final release of the portal planned to become available in early 2017.

Participants at the Seville Workshop, April 2016. Credit: A. Hoffmann

Nonetheless, this beta version already addresses the main aim to offer a unique service for analysing and understanding biodiversity change in Europe. For instance, users can explore how relative abundance of species (within a larger group) changes over time by using big data mediated by GBIF. There is also a spatial browser for locating datasets in any part of the world, which may be usable for computing the EBVs for species populations.

Additionally, an online analytical data processing (OLAP) toolbox has been included in this release. Based on GEOSS technology, the new portal lets users harvest and simultaneously access data from several directories, including GBIF, LTER, EuMon (coming), PESI, and GEOSS sources.

This release also highlights the products of the EU BON project, including new methods and analyses packed in factsheets and infographics for the convenience of scientists and policy users alike. Explore the portal’s beta version here.

Suggestions of how to develop the beta portal further towards the full release are appreciated. Use the feedback form at the welcome page.

Integrated biodiversity data mobilization:

It is a challenge for Bioinformatics group in Europe and around the world to find better ways to integrate different systems and technology. In EU BON’s Task 1.4 the approach to solving this issue was to integrate different systems managing natural history collections and molecular data systems using the best techniques available.

In a dedicated workshop, which took place in Stockholm, Sweden, developers in the sphere of bioinformatics were presented with the project’s Data Mobilization Toolkit. This particular workshop was mainly focused on Docker as a tool to move towards a more integrated environment. Docker has revolutionized system integration and in the workshop the Swedish team shared their experience with dockerizing the DINA-system.

Discussions during the Stockholm workshop; Credit: Karin Karlsson

The workshop ended with a hackathon where they together explored the possibilities for using Docker in selected parts of integrating Pluto-F, JACQ and DINA.

Due to the exponential growth of biodiversity information in recent years, the questions of how to mobilize such vast amounts of data has become more tangible than ever. Best practices for data sharing, data publishing, and involvement of scientific and citizen communities in data generation are the main topic of a recent report by the EU FP7 project Building the European Biodiversity Observation Network (EU BON), published in the innovative Research Ideas & Outcomes (RIO) journal.

The report "Data sharing tools for Biodiversity Observation Networks" provides conceptual and practical advice for implementation of the available data sharing and data publishing tools. A detailed description of tools, their pros and cons, is followed by recommendations on their deployment and enhancement to guide biodiversity data managers in their choices.

"We believe publishing this report in RIO makes a lot of sense given the journal's innovative concept of publishing unconventional research outcomes such as project reports. This feature provides projects like EU BON with the chance to showcase their results effectively and timely. The report provides a useful practical guide for biodiversity data managers and RIO gives the project an opportunity to share findings with anyone who will make use of such information", explains Prof. Lyubomir Penev, Managing Director of Pensoft and partner in EU BON.

The new report is the second EU BON contribution featured in a dedicated project outcomes collection in RIO. Together with the data policy recommendations it provides a comprehensive set of resources for the use of biodiversity data managers and users.

"We did our biodiversity data sharing tools comparison from the perspective of the needs of the biodiversity observation community with an eye on the development of a unified user interface to this data - the European Biodiversity Portal (EBP)", add the authors.

The scientists have identified two main challenges standing in front of the biodiversity data community. On the one hand, there is a variety of tools but none can as stand alone, satisfy all the requirements of the wide variety of data providers. On the other hand, gaps in data coverage and quality demand more effort in data mobilization.

"For the time being a combination of tools combined in a new work-flow, makes the most sense for EU BON to mobilize biodiversity data," comment the report authors on their findings. "There is more research to be done and tools to be developed, but for the future there is one firm conclusion and it is that the choice of tools should be defined by the needs of those observing biodiversity - the end user community in the broadest sense - from volunteer scientists to decision makers."

Original Source:

Smirnova L, Mergen P, Groom Q, De Wever A, Penev L, Stoev P, Pe'er I, Runnel V, Camacho A, Vincent T, Agosti D, Arvanitidis C, Bonet F, Saarenmaa H (2016) Data sharing tools adopted by the European Biodiversity Observation Network Project. Research Ideas and Outcomes 2: e9390. doi: 10.3897/rio.2.e9390

The Biodiversity Indicators Partnership (BIP) Secretariat is looking for indicators to fill gaps in the global suite of biodiversity indicators and allow a full understanding of progress towards globally agreed targets.

They are inviting experts and organisations to participate in an open online consultation to fill the gaps in the global indicator framework for the Strategic Plan for Biodiversity 2011-2020. Through this short online survey they want to hear about any existing indicators (both global and sub-global in scale), indicators under development, potentially useful datasets or key experts or organisations in the fields. The main focus is on indicators that respond to the gaps in the global framework, which are listed on the attached flyer, but they are also keen to hear about any other indicators that could potentially enhance the existing indicator suite.

The consultation is open until 30 June 2016. Further information on the consultation is available in the attached flyer, the BIP website http://www.bipindicators.net/gaps, and the CBD notification SCBD/OES/RH/KNM/85710.

Camera trapping is a powerful and now widely used tool in scientific research on wildlife ecology and management. It provides a unique opportunity for collecting knowledge, investigating the presence of animals, or recording and studying behaviour. Its visual nature makes it easy to successfully convey findings to a wide audience.

The new book provides a much-needed guide to the sound use of camera trapping for the most common ecological applications to wildlife research. Each phase involved in the use of camera trapping is covered:

- Selecting the right camera type 
- Set-up and field deployment of your camera trap 
- Defining the sampling design: presence/absence, species inventory, abundance; occupancy at species level; capture-mark-recapture for density estimation; behavioural studies; community-level analysis 
- Data storage, management and analysis for your research topic, with illustrative examples for using R and Excel 
- Using camera trapping for monitoring, conservation and public engagement.

Each chapter in this edited volume is essential reading for students, scientists, ecologists, educators and professionals involved in wildlife research or management.

Find out more in the promotional video.

About the authors

Francesco Rovero is an ecologist and conservation scientist with a PhD in animal ecology. He is currently the Curator for Tropical Biodiversity at MUSE Science Museum in Trento, Italy. 

Fridolin Zimmermann is a carnivore conservation scientist with a PhD on Eurasian lynx conservation and ecology. He is currently coordinator of the large carnivore monitoring in Switzerland at Carnivore Ecology and Wildlife Management (KORA).

Collectively they have nearly 30 years of professional experience in the use of camera trapping for wildlife research, and have worked on a range of species, habitat and study types.