The Heinz-Nixdorf-Chair for Distributed Information Systems at the Friedrich Schiller University of Jena (Germany) invites applications for a fully funded PhD student position in Biodiversity Data Visualization for the data management project of the Biodiversity Exploratories (BE) Priority Program.

Deadline for application: 2nd, May 2014

Start date: June 2014 or later

What this is about

The data management project provides the platform for data storage and information exchange for the projects of the DFG Priority Program "Biodiversity Exploratories". Examples of the thematic focus of the projects include botany, forestry, soil, animal, fluxes, modeling, and remote sensing. This diversity is reflected in the format, structure, and semantics of their data which we manage.

Tasks in this project will be centered on the investigation and development of novel visualization methods and user-friendly tools for exploration, search and discovery, quality assurance and integration of the heterogeneous, large volume biodiversity data.  Overall, the study should contribute to the science of visualization for big-data-driven biodiversity research.

More information on the requirements, conditions and how to apply find in the official job offer attached below.

The April 2014 mirror updates of FishBase (www.fishbase.ca and www.fishbase.us); are now available online.

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

The "Building the European Biodiversity Observation Network" EU BON General Meeting took place between 30 March - 3 April 2014 in Heraklion on Crete, to present major project results and set objectives for the future. The meeting was preceeded by a review paper recently published in the open access journal Nature Conservation, to point out EU BON researchh interests and objectives for the future of biodiversity protection.

This is a group photo of the participants in the recent EU BON General Meeting in Crete, Greece.

The 2014 General Meeting brought together keynote speakers Jörg Freyhof (GEO BON, Executive Director), Marc Paganini (European Space Agency), Jerry Harrison (UNEP-WCMC) with the entire EU BON consortium to discuss collaborations between the project and other important initiatives in the areas of earth observation, particularly in remote sensing and in situ approaches to biodiversity data collection, as well as in the use and analysis of biodiversity data for forecasting and scenario building, and environmental policy.

"The high potential for satellite Earth Observations to support biodiversity monitoring is growing but is yet to be fully realised. The recent efforts of GEO BON, supported by the GEO Plenary and the CBD Conference of the Parties, to define a set of minimum essential observational requirements to monitor biodiversity trends will give considerable impetus for space agencies and for the remote sensing community to focus their work on a small set of well defined earth observations products that will serve the needs of the biodiversity community at large. In that context ESA is firmly engaged in supporting the development of these emerging Essential Biodiversity Variables (EBVs). EU BON together with ESA can be pioneers in the early development and demonstration." comments Marc Paganini, European Space Agency, on the future collaboration between the two initiatives.

The world's biodiversity is in an ongoing dramatic decline that despite conservation efforts remains unprecedented in its speed and predicted effects on global ecosystem functioning and services. The lack of available integrated biodiversity information for decisions in sectors other than nature conservation has been recognized as a main obstacle and the need to provide readily accessible data to support political decisions has been integrated into the CBD's "Strategic Plan for Biodiversity 2011–2020" and the Aichi targets. The recently published EU BON review paper points out how the project will use its potential to improve the interaction between citizens, science and policy for a better future of biodiversity protection.

EU BON aims to enable decision makers at various levels to make use of integrated and relevant biodiversity information adapted to their specific requirements and scales. Disparate and unconnected databases and online information sources will be integrated to allow improved monitoring and evaluation of biodiversity and measures planned or taken at different spatial and temporal scales. This requires strong efforts not only with regard to technical harmonization between databases, models, and visualization tools, but also to improve the dialogue between scientific, political, and social networks, spanning across several scientific disciplines as well as a variety of civil science organizations and stakeholder groups.

The project is focusing mainly on the European continent but contributes at the same time to the globally oriented Group on Earth Observations Biodiversity Observation Network (GEO BON), which itself contributes to the Group of Earth Observation System of Systems (GEOSS). EU BON will build on existing information infrastructures such as GBIF, LifeWatch and national biodiversity data centres in Europe, and will integrate relevant biodiversity data from on-ground observations to remote sensing information, covering terrestrial, freshwater and marine habitats.

Original Source:

Hoffmann A, Penner J, Vohland K, Cramer W, Doubleday R, Henle K, Kõljalg U, Kühn I, Kunin WE, Negro JJ, Penev L, Rodríguez C, Saarenmaa H, Schmeller DS, Stoev P, Sutherland WJ, Ó Tuama É, Wetzel FT, Häuser CL (2014) Improved access to integrated biodiversity data for science, practice, and policy - the European Biodiversity Observation Network (EU BON). Nature Conservation 6: 49–65. doi: 10.3897/natureconservation.6.6498

The European Space Agency (ESA) is Europe’s gateway to space. Its mission is to shape the development of Europe’s space capability and ensure that investment in space continues to deliver benefits to the citizens of Europe and the world.  ESA is an international organisation with 20 Member States.

How is EU BON connected to space research? As a speaker at the EU BON General Meeting, which took place on Crete between 30 March - 3 April 2014, Marc Paganini of the European Space Agency explains the collaboration between ESA and GEO BON, and how EU BON is involved.

In the following interview he continues the topic:

Marc Paganini (left) and Dirk Schmeller (right) at the EU BON General Meeting 2014

1) For most of the general public space and biodiversity research hardly have anything to do with each other, can you explain how the European Space Agency (ESA) and the idea of remote sensing communities make these two meet?

It is widely recognized that in-situ observations available on biological diversity are very scarce for most of the Earth’s ecosystems and are often insufficient for determining precisely the global status and trends of biodiversity worldwide. In most cases, satellite Earth Observations do not provide a direct measurement of biodiversity but, if properly used with ground collection of biodiversity data and species and habitat modeling, remote sensing can become an important and essential component of biodiversity monitoring systems. There are multiple cases where remote sensing is often the only instrument that can offer large scale monitoring, as for example in highly variable ecosystems such as wetlands or in remote areas that can hardly be monitored by field campaigns.

The recent and future evolution of the portfolio of EO satellites offers huge potential for increasing the use of EO products into biodiversity monitoring systems. The lack of data continuity has always been a barrier for the biodiversity community to invest in EO technology.  A commitment from Space Agencies to provide sustained observations on the long term is a strong incentive for the biodiversity community to invest in Space. The Sentinel series of the European Copernicus program, together with the freely available data from other space agencies such as the Landsat family of the US Geological Survey, will bring unprecedented long-term continuity of observations for the biodiversity community. In that context, free and open data policy to taxpayer-funded satellite remote sensing imagery is becoming a "de facto" standard amongst Space Agencies and a unique opportunity for the biodiversity community to use widely EO products to monitor biodiversity trends.

2) How is the ESA involved with the aims of EU BON, where do the two initiatives intersect?

ESA and many other Space Agencies are becoming more and more committed in helping the biodiversity community at large, in improving their capacity to use remote sensing data for monitoring biodiversity trends.

First there is a coordinated action from all Space Agencies through the Committee on Earth Observation Satellites (CEOS) and its involvement in the Group of Earth Observation (GEO). The GEO is a voluntary partnership of governments and international organizations who engaged jointly in developing a comprehensive, coordinated and sustained system of observations of the Earth with the ultimate objective to enhance scientifically-sound decision making. Biodiversity is one of the primary societal benefit areas of GEO and is addressed by the GEO Biodiversity Observation Network (GEO BON). CEOS is actively involved in GEO BON, principally through the participation to its steering committee of the European, US and German Space Agencies, namely ESA, NASA and DLR. Since EU BON is the principal European contribution to GEO BON, and has, amongst its objectives, the aim to integrate biodiversity data from ground observations to remote sensing information, ESA is directly concerned by the EU BON development in using remote sensing for terrestrial, freshwater and marine realms.

Second, ESA has its own EO application development programs, and funds a wide range of Research & Development projects for biodiversity and ecosystem services. In that context, ESA has established close relationships with the European Environment Agency (EEA) but also with the secretariats and scientific bodies of major Multilateral Environmental Agreements (MEA) such as the Convention on Biological Diversity (CBD) and the Ramsar Convention on wetlands. The findings of the ESA-funded EO projects on biodiversity and ecosystem services are highly relevant to EU BON. It is therefore expected that the ESA and EU BON activities in relation to the use of RS for biodiversity monitoring will offer some convergence of evidence showcases for the whole biodiversity community.

3) How do you see the future of collaboration with EU BON?

The high potential for satellite Earth Observations to support biodiversity monitoring is growing but is yet to be fully realised. The recent efforts of GEO BON, supported by the GEO Plenary and the CBD Conference of the Parties, to define a set of minimum essential observational requirements to monitor biodiversity trends will give considerable impetus for space agencies and for the remote sensing community to focus their work on a small set of well defined EO products that will serve the needs of the biodiversity community at large. In that context ESA is firmly engaged in supporting the development of these emerging Essential Biodiversity Variables (EBVs). EU BON together with ESA can be pioneers in the early development and demonstration.

Hoffmann A, Penner J, Vohland K, Cramer W, Doubleday R, Henle K, Kõljalg U, Kühn I, Kunin WE, Negro JJ, Penev L, Rodríguez C, Saarenmaa H, Schmeller DS, Stoev P, Sutherland WJ, Tuama1 EO, Wetzel F, Häuser CL (2014) Improved access to integrated biodiversity data for science, practice, and policy - the European Biodiversity Observation Network (EU BON). Nature Conservation 6: 49–65. doi: 10.3897/natureconservation.6.6498

Researchers and the public can now have immediate access to data underlying discovery of new species of life on Earth, under a new streamlined system linking taxonomic research with open data publication.

The partnership paves the way for unlocking and preserving a wealth of 'small data' backing up research conclusions, which often become lost within a few years of an article's publication in an academic journal.

In the first example of the new collaboration in action, the Biodiversity Data Journal carries a peer-reviewed description of a new species of spider discovered during a field course in Borneo just one month ago. At the same time, the data showing location of the spider's occurrence in nature are automatically harvested by the Global Biodiversity Information Facility (GBIF), and richer data such as images and the species description are exported to the Encyclopedia of Life (EOL).

This contrasts with an average 'shelf life' of twenty-one years between field discovery of a new species and its formal description and naming, according to a recent study in Current Biology.

A group of scientists and students discovered the new species of spider during a field course in Borneo, supervised by Jeremy Miller and Menno Schilthuizen from the Naturalis Biodiversity Center, based in Leiden, the Netherlands. The species was described and submitted online from the field to the Biodiversity Data Journal through a satellite internet connection, along with the underlying data . The manuscript was peer-reviewed and published within two weeks of submission. On the day of publication, GBIF and EOL have harvested and included the data in their respective platforms.

The new workflow established between GBIF, EOL and Pensoft Publishers' Biodiversity Data Journal, with the support of the Swiss NGO Plazi, automatically exports treatment and occurrence data into a Darwin Core Archive, a standard format used by GBIF and other networks to share data from many different sources. This means GBIF can extract these data on the day of the article's publication, making them immediately available to science and the public through its portal and web services, further enriching the biodiversity data already freely accessible through the GBIF network. Similarly, the information and multimedia resources become accessible via EOL's species pages.

One of the main purposes of the partnership is to ensure that such data remain accessible for future use in research. A recent study published in Current Biology found that 80 % of scientific data are lost in less than 10 years following their creation.

Donald Hobern, GBIF's Executive Secretary, commented: "A great volume of extremely important information about the world's species is effectively inaccessible, scattered across thousands of small datasets carefully curated by taxonomic researchers. I find it very exciting that this new workflow will help preserve these 'small data' and make them immediately available for re-use through our networks."

"Re-use of data published on paper or in PDF format is a huge challenge in all branches of science", said Prof. Lyubomir Penev, managing director of Pensoft and founder of the Biodiversity Data Journal. "This problem has been tackled firstly by our partners from Plazi who created a workflow to extract data from legacy literature and submit it to GBIF. The workflow currently launched by GBIF, EOL and the Biodiversity Data Journal radically shortens the way from publication of data to their sharing and re-use and makes the whole process cost efficient", added Prof. Penev.

The elaboration of the workflow from BDJ and Plazi to GBIF through Darwin Core Archive was supported by the EU-funded project EU BON (Building the European Biodiversity Observation Network, grant No 308454). The basic concept has been initially discussed and outlined in the course of the pro-iBiosphere project (Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination, grant No 312848).

Original source:

Miller J, Schilthuizen M, Burmester J, van der Graaf L, Merckx V, Jocqué M, Kessler P, Fayle T, Breeschoten T, Broeren R, Bouman R, Chua W, Feijen F, Fermont T, Groen K, Groen M, Kil N, de Laat H, Moerland M, Moncoquet C, Panjang E, Philip A, Roca-Eriksen R, Rooduijn B, van Santen M, Swakman V, Evans M, Evans L, Love K, Joscelyne S, Tober A, Wilson H, Ambu L, Goossens B (2014) Dispatch from the field: ecology of micro web-building spiders with description of a new species. Biodiversity Data Journal 2: e1076. DOI: 10.3897/BDJ.2.e1076

Issue 72 of the CBD Technical Series is now out focusing on "EARTH OBSERVATION FOR BIODIVERSITY MONITORING : A review of current approaches and future opportunities for tracking progress towards the Aichi Biodiversity Targets". The issue shows how earth observation technologies can and should fit into systems for biodiversity monitoring, as well as demonstrates how these approaches could further improve relevant indicators for the Aichi Biodiversity Targets. It illustrates a clear track from observations done by remote sensing platforms through Essential Biodiversity Variables to biodiversity indicators and ultimately to the assessment of progress towards the Aichi Biodiversity Targets and ultimately in support of evidence-based decision making. EU BON is also featured in this report.

The goal of the CBD Technical Series is to contribute to the dissemination of up-to-date and accurate information on selected topics that are important for the conservation of biological diversity, the sustainable use of its components and the equitable sharing of its benefits. A large and growing body of evidence has clearly established the need to disseminate synthesis publications relevant to CBD objectives and selected reports presented at CBD meetings.

The CBD Technical Series is intended to:

• Foster scientific and technical cooperation;
• Improve communication between the Convention and the scientific community;
• Increase awareness of current biodiversity-related problems and concerns; and
• Facilitate widespread and effective use of the growing body of scientific and technical information on conserving and using biological diversity.

The full report is available here.

The SUSTAIN EU-ASEAN project aiming at establishing a more sustainable and integrated research and innovation cooperation between the EU and the ASEAN region in the areas of climate action, resource efficiency and raw materials has now published its first project newsletter.

This first issue of the SUSTAIN EU-ASEAN Newsletter contains information about the outcomes from the first project Networking and Cluster Session that took place on 23 January 2014 in Bangkok, Thailand, as well as features a news item about the forthcoming sessions scheduled for 28 Match 2014 in Brussels, Belgium. More can be found in the Newsletter available here.

The SUSTAIN EU-ASEAN coordinating action will focus on climate action, resource efficiency and raw materials issues and will aim to enhance collaboration between researchers in the EU and the ASEAN region. Addressing these issues in a coherent way is vital for sustainable development that leads to economic prosperity, social cohesion and environmental integrity. Both regions have developed innovative ideas to reduce greenhouse gas emissions, to adapt to climate change, improve resource efficiency and manage raw materials.

Care about biodiversity protection and science-policy dialogue? The second BESAFE stakeholder workshop might be just the thing for you.

The BESAFE project invites all interested policy makers, NGO representatives, decision makers and people, who argue ('lobby') for biodiversity protection to take part in its second stakeholder workshop, focusing the results from the project case studies and the best ways to make them useful through a stakeholder focused web-based tool.

The workshop will be held on 13 and 14 May 2004 at the Park Inn Brussels Midi, Brussels, Belgium. To register and participate is easy just follow this link, which will take you to an easy to follow and use registration page.

On the afternoon of 13 May BESAFE will present the results of the project’s case studies and then their use and implications will be discussed with stakeholders. The morning of 14 May is reserved for a learning workshop on the best ways to unlock and present project results. As committed stakeholder involvement is crucial to BESAFE’s success, we hope that you will be able to join us in Brussels!

In a nutshell, BESAFE investigates the effectiveness of different types of arguments in convincing policy makers to take action for biodiversity protection in a variety of circumstances. The project has two specific focus areas: the interactions of environmental protection policies between governance scales, and the contribution that ecosystem services BESAFE is committed to produce practically usable results and to make them available and easily accessible through a web-based tool. This is a goal we can clearly only achieve through input and feedback from stakeholders. BESAFE is therefore set up as an interactive project in which we inform and consult those on a regular basis.

Deadline for registration is the 1st of April 2014, but registration will be closed earlier when our limit of 25 stakeholders is reached. Due to this limited capacity, registration is subject to approval.

The ASEAN-EU STI Days took place between 21-23 January 2014 in Bangkok, Thailand.  During the event a special workshop "Integration of biodiversity data recording and information management systems for environmental sustainability: a call for EU-ASEAN collaboration" has been organized to stimulate EU-ASEAN collaboration in research on biodiversity informatics and integrative environmental information management.

A special EU BON dedicated presentation was given by Dr. Christoph Häuser at the workshop, which took place on 22 January. As a regional component of the Group of Earth Observation Biodiversity Observation Network (GEO BON), the EU BON project presented an innovative approach towards integration of biodiversity information systems from on-ground to remote sensing data, for addressing policy and information needs in a timely and customized manner.

Such an approach requires integration between social networks of science and policy, and technological networks of interoperating IT infrastructures. While focussing on Europe, EU BON is expected to connect and reach out globally, especially towards regions with many biodiversity hotspots such as SE-Asia.

The main objectives of the workshop were to:

• Review and compare the situation regarding relevant biodiversity and Earth observation data and information sources/providers in EU and ASEAN;
• Examine linkages between regional/national ASEAN and EU efforts with international / global biodiversity information systems (in particular GBIF, GEO BON);
• Assess and discuss national vs. regional level priorities and needs with regard to integrated biodiversity information in ASEAN and Europe;
• Identify common challenges and needs towards further integration of different types, levels, and scopes of available data and information systems;
• To address how S&T cooperation between Europe and ASEAN in the area of biodiversity and Earth observation could be further developed to better serve policy needs (especially in light of IPBES), and to contribute to common goals towards sustainable economic development.

Five other presentations were given at the workshop on behalf of Global Biodiversity Information Facility (GBIF), ASEAN Centre for Biodiversity (ACB), FishBase Information and Research Group, Forest Research Institute Malaysia (FRIM), National Center for Genetic Engineering and Biotechnology (BIOTEC), and Thailand Bioresource Research Center (TBRC). Presentations from the meeting are available to view below, or alternatively visit: http://www.stidays.net/?page_id=510

Presentations:

Christoph L. Häuser (EU BON) on "The EU BON approach for information integration" (introduction to the workshop)

Tim Hirsch (GBIF) on "The Global Biodiversity Information Facility (GBIF) – collaborating to promote data access for research and policy"

Sheila G. Vergara (ACB) on "Knowledge sharing for biodiversity conservation in the ASEAN Region"

Christine Casal (FishBase) on "Using FishBase and AquaMaps to predict IAS establishment, species ranges and risk assessment"

Leng Guan Saw (FRIM) on "Herbarium Data and Plant Conservation in Malaysia"

Lily Eurwilaichitr (TBRC) on "TBRC as an online information intermediary: towards the sustainability of biological resources"

ANNOUNCEMENT: The February 2014 update of the FishBase (www.fishbase.us and www.fishbase.ca) and SeaLifeBase (www.sealifebase.ca) websites are now available online.

FishBase stats to date: (32700 Species, 302900 Common names, 53600 Pictures, 49700 References, 2100 Collaborators, 700000 Visits/Month)

SeaLifeBase stats to date: (126000 Species, 27300 Common names, 11900 Pictures, 18200 References, 250 Collaborators)

EU BON takes care to enhance the expertise of its consortium by affiliating associate partners, an approach the project is planning to continue with. EU BON is pleased to welcome the latest addition to our list of associate partners - HaMAARAG- The Israel National Program for Ecosystem Assessment.

HaMaarag was established in 2006, following a decade’s worth of research in Long Term Ecological Research (LTER) stations. Its main objective is to promotescience-based management of open landscapes and natural resources, for human well-being and for long-term sustainability of nature in Israel.

HaMaarag aims to:
•   Generate science-based knowledge about the state of ecosystems and biodiversity in Israel
•   Strengthen the relationship between scientific knowledge, management and policymaking, in the fields of natural resource and open landscape management, land use planning and nature conservation.
•   Improve accessibility of this knowledge to decision-makers and the general public.

By achieving these aims, HaMaarag promotes the development of a common language, knowledge base and perspective regarding ecosystems in Israel, thus facilitating efficiency of management and policy within the relevant organizations.

The official kick-off of the EU BON project WP6 Stakeholder engagement and science-policy dialogue and WP7 Implementation of GEO BON: strategies and solutions at European and global levels took place on 18-19 February 2014 in Leipzig, Germany. The two work packages are a crucial part of the project outlining the future actions towards ensuring the integration of the project with its global counterpart GEO BON, as well as paving the road towards successful stakeholder and policy engagement.

As a result of this first meeting further short-term and long-term steps were outlined for WP6 and WP7 towards the achievement of main project objectives. These steps include shaping the future EU BON GEO BON interactions and EU BON’s approach towards stakeholder engagement.

In the following interview Ilse Geijzendorffer gives an insight on the outcomes from the meeting.

This image shows the discussions during the WP6/WP7 kick-off meeting. Credit: Eugenie Regan

1) What are the project’s main stakeholders that you are planning to approach and interact with in the future?

EU BON aims to develop a blue print for a data infrastructure for data handling, storage, indicator computation and transfer of knowledge via a data portal available to knowledge seekers. This data infrastructure thus has to be useful to data holders who want their data to be used (e.g. citizen scientists, nature associations, scientists) and to those that seek knowledge (e.g. reporting bodies). EU BON reaches out to these stakeholders and to bodies that would be interested to host or have such a data infrastructure themselves. Our first stakeholder round table focused on European knowledge seekers and existing data portals. Our second stakeholder round table planned for this summer will focus on citizen scientists and the organisations that currently handle the citizen science data, to receive input on what these two stakeholder groups would like to see in such a data infrastructure blue print.

At the same time we reach out to ongoing platforms that consist of networks of knowledge and that have needs regarding their data flow. A very important partner in the data infrastructure development is GEO BON. The coordination of GEO BON has just changed and EU BON will reinforce the ties with GEO BON during the General Assembly in Crete coming in April.

2) Science-policy dialogue proves to be a crucial part for the success of large scale projects like EU BON, how are you tackle this challenge?

The objective of EU BON is a moving target in the sense that the blue print for data infrastructure will need to suit the needs for current and future monitoring. Additionally, the actual implementation, funding and hosting of such an infrastructure could be within a structure that may not yet exist in that form today. Changes in mission, coordination and targets occur constantly. To profit from lessons learned, we are in close contact with the Biodiversity Knowledge Project; a project that has already gained experience in the last four years in identifying the most important elements for handling data requests from knowledge seekers and in developing a suitable management plan.

For EU BON to achieve and reach its moving target, we keep in touch with the changes within the biodiversity knowledge landscape (e.g. progress in IPBES, CBD reporting, European targets ad evaluations); we explore multiple scenarios for the data infrastructure, the business plan and the implementation options; and we collaborate with a large range of stakeholders to include not only their ideas and needs, but also the transitions that they go through.

A joint EU BON WP3-WP4 meeting took place on 25-27 November 2013 in Solsona, Spain. The main aim of the meeting was to officially kick off WP3 and provide forum for discussion of the planned work. The two work packages were presented with their main aims, scope and objectives. The place of the two work packages in the broader framework of EU BON, and the cross-links between the two, were also discussed.

In the following interview Hannu Saarenmaa and Klaus Henle share insights from the meeting:

1) WP3 ‘Improving tools and methods for data analysis and interface’ and WP 4 ‘Link environment to biodiversity: analyses of patterns, processes and trends’ are two of the core work packages in EU BON that are expected to accumulate a lot of genuine data and develop new tools for data analysis and interface. Can you explain in short what will your main activities involve?

HS: I can contribute to the project and these WPs a large-scale modelling technology from the BioVeL project that can process hundreds of species. This would be an engine to compute the first real Essential Biodiversity Variables (EBV).

KH: Our main activities will involve an analysis how available effort is best allocated in time and space to optimize results from monitoring. We will further assess how different sources of uncertainty influence conclusions derived from the analysis of monitroing data

2) What were the main results of the meeting in terms of the planned work and WP management?

HS: It was proposed to set up an EBV Task Force across the EU BON project.  If we can do that, it would really give a thrust for the project. If we could pick up the Database of Monitoring Schemes from the EUMON project, as discussed, that would give us access to some large datasets.

KH: One main result was the identification of the concrete responsibilities (e.g. data provision, data analysis for terrestrial, freshwater and marine biodiversity) within the workpackage and to identify explicitly links to other workpackages.

3) What novelty will the work in these two work packages bring and what will the major results be?

HS: If they can create a new Ecological Niche Modelling algorithm that can also deal with spatial patterns, that would be interesting.  Such a model actually exists in MigClim, but it is not yet widely used.

KH: We will get recommendations how monitoring can be optimized and a more comprehensive understanding of changes in biodiversity and their underlying causes

4) What are the immediate planned activities and when can the first results be expected?

KH: The most immediate planned activities it the screening of potentially available data needed for the analysis

5) How will the WP3/4 interact with GEO BON?

HS: The proposed EBV Task Force would need to interface very closely with GEO BON.

KH: We are engaged directly with key members of GEO-BON; e.g. we have regular meetings with Henrique Perreira.

An international conference Adaptation Strategies to Global Environmental Change in the Mediterranean City and the Role of Global Earth Observations will take place between 10-11 June 2014 in Athens, Greece. The conference will explore the potential of earth observations and thrust climate information transfer from the science to the stakeholder application realm, in order to develop suitable adaptation measures at national and regional levels.

It will identify best adaptation programs and approaches to global environmental change in Mediterranean-climate cities. The aim is to enhance and strengthen European and international cooperation in the context of the activities within the Group on Earth Observations (GEO), and promote tools and options for adaptation strategies. The Conference will help local and regional authorities and stakeholders to gain insight on the role of EO-based services in adapting to climate chance impacts in urban hot-spot areas.

The eighth annual series of GEO European Projects Workshops will be consequently held on 12-13 June as a follow-up of the conference. The worksops are intended to bring all those interested in and actively contributing to the Global Earth Observations System of Systems (GEOSS) from all over Europe together, in order to present their work and discuss how Europe can contribute to this international effort, especially in the wake of the launch of the new EU Framework Programme for Research, Horizon 2020, and the renewal of the mandate of GEO for another 10 years through the endorsement of the 2014.

Registrations opens: 16 February 2014

Information and registration: www.mariolopoulosfoundation.gr/medcity2014

First Announcement (pdf flie)

Following the GEO-X Plenary in Geneva earlier this year (15-16 January 2014), GEO now issues Revision 3 of the GEO 2012-2015 Work Plan incorporating comments from the meeting. The new work plan is available through the GEO Work Plan Information Management system.

The GEO Work Plan provides the agreed framework for implementing the GEOSS 10-Year Implementation Plan (2005-2015). It is a living document that is updated annually. The 2012-2015 Work Plan has been designed to meet the 2015 GEOSS Strategic Targets. As a result, the tasks of the Work Plan correspond to outcomes identified as being necessary to meet the Strategic Targets.

The highlighted actions in the revised work plan are as follows:

• Call for Participation (CFP) in the 6th phase of the GEOSS Architecture Implementation Pilot (AIP)
• GEOSS Common Infrastructure (GCI) - Initial Operating Capability (IOC) phase
• Data Sharing Principles implementation
• AIP information page to GEOSS Implementation
• Call for Proposals: Earth Observations in Decision Support Projects

The GEO Work Plan provides a flexible action-oriented framework for developing new projects within and across areas, and coordinating strategies and investments. Benefits and opportunities include inter-alia: fostering networking and partnerships (new contacts and collaborations); launching regional and/or global initiatives (e.g. GEO BON, GEOGLAM); providing access to data (making more data available); enlarging user-bases (users grow in numbers and diversity); developing and maintaining capacity (participants build on complementarity); increasing visibility and high-level support (e.g. through the GEO Website, Newsletter, Plenary, Ministerial); and leveraging funding for activities (funding mechanisms value contributions to GEOSS implementation, like the European 7^th Framework Programme).

EU BON site data management workshop and Memorandum of Understanding

A joint workshop of the Sierra Nevada LTER site and EU BON was held on 29-31 January 2014 in Granada, Spain and was hosted by the University of Granada. The aim of this meeting was to bring together the Spanish members of the Sierra Nevada LTER site and test site partners from EU BON (WP1, WP2 and WP5) to discuss and develop a closer relationship in exchanging datasets and experiences in site management, long-term monitoring activities and technical requirements for data management.

During the first day of the workshop, 19 participants from EU BON, the Sierra Nevada LTER site (e.g. Regino Zamora Rodriguez and Francisco Bonet) and guests from the remote sensing EU project BIO_SOS and GBIF Spain gave an overview of their activities to obtain information on their projects and to point out likely synergies and linkages. First, the Sierra Nevada LTER site was introduced, particularly the methodologies to monitor and evaluate biodiversity and the structure of the information system Linaria was shown. Thereafter EU BON testing sites (Doñana, Rhine-Main, Amvrakikos) outlined their current activities regarding data collection, data processing and data integration, in addition to that the results of a recently conducted gap analysis of the test sites were presented. In the afternoon session of the meeting, the planned information architecture of EU BON was explained and ways outlined of how biodiversity data could be integrated.

At the second day, the participants visited a highly monitored area located in the southern part of Sierra Nevada (Alpujarras) that is covered mainly by Quercus pyrenaica forests. The field trip included stops at a meteorological station, a traditional hydrological system was visited to show former human impact in the area and the functionality of a field NDVI camera was shown. This site-trip was also used to officially hand-over the Memorandum of Understanding, signed between the University of Granada and EU BON, to strengthen the cooperation between the Sierra Nevada LTER and the EU BON test sites. Anke Hoffmann on behalf of EU BON handed the MoU to Professor Regino Zamora Rodriguez, the scientific coordinator of the Sierra Nevada Global Change Observatory. The University of Granada is now a new associate partner of EU BON, a consortium with currently 30 partners from 18 countries.

At the last day local scientists gave an overview of the research conducted in Sierra Nevada. After that session, the workshop aimed to discuss the functionality of the envisaged MetaCat (dataprovider for Metadata) approach for the EU BON test sites and the advantages of self-developed information system Linaria of the Sierra Nevada LTER site.

EU BON will further intensify the dialogue with the University of Granada and the Sierra Nevada LTER site. It is scheduled to have a further meeting at the upcoming General Meeting of EU BON (Greece, 30 March-2 April 2014) to strengthen the partnership with the LTER test site.

For further questions please contact Anke Hoffmann or Florian Wetzel

Presentations from the meeting:

Day 1

1. Zamora - Ramos - Sierra Nevada global change obs
2. Bonet - The Linaria information system
3. Hoffmann - Häuser - Introduction to EU BON
4. Juan Negro  - CSIC-EBD
4. Juan Negro Donana 2
4. Juan Negro Donana 3
5. Stoll - test site Rhein - Main
6. Dailianis - test site Amvrakikos
7. Wetzel - Gap analysis
8. Palma Blonda - BIO_SOS and remote sensing
9. Pando - EU BON GBIF Granada 2014
10. Kunin- EU BON Work package 3

Day 3

1. Megia - Mendenez - Climate Change andd elevational range shifts
2. Gomez - Hybridization
3. Villar - Argaiz  Long time series in high mountain lakes
4. Moreno - Vegetation changes during Holocene

Workshop Agenda

Workshop Minutes

Workshop Photos (Google+ | Facebook)

Ecosystem functioning, or the role which organisms play in an ecosystem, is becoming increasingly important in marine ecological and conservation. To facilitate such studies an international team of scientists lead by S. Faulwetter from the Hellenic Centre for Marine Research (HMRC) present the Polytraitsdatabase that aims to provide re-usable, and accessible data on marine bristle worms. The paper describing the new database was published in the innovative Biodiversity Data Journal, a pioneer in the publication of integrated biological data.

Benthic organisms participate in a number of biological processes in world water basins. Their functional diversity is an important community property demonstrating the role organisms have in the ecosystem and helping to understand how the community reacts to environmental changes. Polychaetes, or bristle worms, are marine worms famous for their peculiar shapes and often vivid coloration. More than 10,000 species are described in the class worldwide, most of which living in the shelf zone of the seas and oceans, burrowing in the sediment or swimming among the plankton.

At present, the Polytraits database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 species, all referenced by literature sources. All data on these engaging organisms can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable. The new database presents a rich and easy to use collection, which cover morphological, reproductive and behavioural characteristics of polychaetes, as well as information on environmental preferences in an attempt to facilitate ecological research and conservation studies.

The researchers also provide a leading-edge approach to accessing, integrating and re-using the data. Through programming interfaces, the life-cycle information is automatically integrated into the Polychaetes Scratchpads, together with other data on polychaetes. Scratchpads are easy to use, adaptable, and provide powerful tools for managing biodiversity data. This taxon-centric virtual research environment allows browsing the taxonomic classification and retrieving various kinds of relevant information for each taxon, among which are also the collected biological traits.

Furthermore, the data are also accessible through Encyclopedia of Life's TraitBank which currently features over 3 million records related to more than 250 attributes for 272,720 taxa, including the Polytraits data. TraitBank serves as a provider for aggregated species trait data. All data uploaded there are archived and integrated with trait information from other sources to address issues of standardization of scientific data. This is the first complex database for marine organisms to be published in such an innovative way and demonstrates yet another example of collaboration between the data publisher Pensoft and Encyclopedia of Life.

The second plenary of the Platform met in December 2013 and agreed an ambitious work programme for 2014-2018: Details of the agreed work programme are available in the advanced meeting report of the Plenary.

The IPBES Secretariat have now issued a call for experts to help scope, advise on and deliver the work programme. Governments and relevant stakeholders can put forward nominations, from which the Multidisciplinary Expert Panel of IPBES will select a maximum of 20% of experts from the stakeholder nominations, and the rest from the government nominations.

The UK expects IPBES to make use of the best scientists/experts from all relevant disciplines - natural science, social science, economics, data and modelling and traditional knowledge, and to achieve a geographical and gender balance among those experts in the delivery of the IPBES work programme.

More information of the required topics to be covered by experts, alongside the nomination forms and how to nominate can be found in the attachments below.

On the 17 Jan in Geneva, the Group on Earth Observations (GEO) received unanimous endorsement to unleash the power of open data for a second decade. There was agreement to continue building on the organization’s first 10 years of pioneering environmental advances, which are designed to improve the quality of life of people everywhere. Fueled by open data, GEO’s efforts are now evident in most regions of the world. GEO is comprised of 90 member nations, the European Commission and 77 Participating Organizations.

"GEO is successfully meeting its mandate, which is to make data and other information open, accessible and easy to discover for decision makers around the world," said Mr. Janez Potočnik, European Commissioner for the Environment. "GEO’s vision is now operational, a proven force for putting sound science to work across nine essential areas: agriculture, biodiversity, climate, disasters, ecosystems, energy, health, water and weather."

GEO’s mandate is to drive the interoperability of the many thousands of space-based, airborne and in situ Earth observations around the globe. Without concerted efforts to coordinate across diverse observations, these separate systems often yield just snapshot assessments, leading to gaps in scientific understanding and hampering data fusion in support of better decision making for society. GEO aims to fill such gaps by providing a comprehensive, more integrated picture of our changing Earth. GEO is accomplishing this by establishing a Global Earth Observation System of Systems, known as GEOSS, and a Portal through which data and other information can be easily accessed at little or no cost.

"Rather than snapshot assessments, GEO gives us moving pictures of a changing planet," said Mr. Cao Jianlin, Vice Minister of the Ministry of Science and Technology of China. "Our world does not work just in the sea, on land, in the atmosphere or in space, and our policies cannot reflect individual domains either."  China, for example, is partnering with 46 other GEO-member nations and several of GEO’s Participating Organizations to ensure that unprecedented data will be available to measure the effects of human activities and natural processes on the carbon cycle, the first such coordinated effort at the global level.

In South Africa, 22 nations and 5 GEO Participating Organizations recently launched AfriGEOSS with the goal of strengthening that continent’s capabilities to produce, manage and use earth observations. "This new initiative gives us the necessary framework to support informed decisions about a range of priorities, including food security, access to clean water and sanitation, natural resources, and coastal and disaster management," said Derek Hannekom, Minister of Science and Technology, South Africa.

By increasing the utility of open data about the Earth, GEO is helping to mitigate disasters, develop water-management strategies, support citizen observatories, and strengthen food security. GEO is driving the development of new tools, such as a cholera early warning system, as well as painting fuller pictures of complex environmental processes, including through global observations of ocean acidification at the global scale and observations of atmospheric greenhouse gases from space. GEO participants are also studying the footprint of mining practices, with the aim of minimizing future impacts on nearby communities and natural habitat, and focusing on links between air quality and health. There is also focus on the far-reaching consequences of melting glaciers and other serious cold-region concerns.

"The Obama Administration continues to work to catalyze the emergence of new businesses, products and services powered by the U.S. Government's open data. Increasing access to data and data sharing, both nationally and internationally, is crucial for unleashing innovation across our data-driven economy," said Dr. Patrick Gallagher, performing the duties of the Deputy Secretary of Commerce." GEO's collaborative work to integrate open data about the Earth continues to drive the development of new tools, services and scientific insights that are used around the world to support sound decision making."

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 36-months PhD position open for applications. The position is funded by the European Commission through the FP7 Research Project OPERAs and affiliated to the French National Scientific Research Centre (CNRS).

The topic is the broad-scale spatial mapping and quantification of ecosystem service trade-offs following from management of agro-ecosystems in the Mediterranean basin. The context of the research includes the environment (climate, land use) as well as trends in societal demands for services. Based on scientific literature, spatial databases and the outputs from a process-based ecosystem model, the candidate will analyze, quantify and map ecosystem service trade-offs. Service valuation and indicator representation methods will be developed with the IMBE team. The approach is pan-Mediterranean: a significant part of the work will therefore consist of helping to reduce gaps in data and knowledge for the sum of countries around the Mediterranean basin. 

The research group works in close interaction with international programs such as Future Earth (through its project ecoSERVICES) and science-policy interfaces such as IPBES.

The successful candidate will have completed a Masters degree (or equivalent) in one of the environmental sciences, have experience in the handling of spatial data from databases, literature and models, have knowledge of existing concepts of ecosystem services, and be able to place results in the context of the Mediterranean basin (this includes the European, as well as North African and Eastern countries). The working language is English, appropriate skills in French or another of the Mediterranean languages will be an advantage.

The position will be filled when a suitable candidate has been identified. To apply for this position, please send a letter of application, demonstrating your ability to understand the task, and your CV as soon as possible, but before the 31st of January 2013, by e-mail to Ms. Gabriela Boéri (Gabriela.Boeri@imbe.fr). For any questions about the task, working conditions, or the OPERAs project, please contact Professor Wolfgang Cramer (Wolfgang.Cramer@imbe.fr).

The ASEAN-EU Science, Technology and Innovation (STI) Days will take place between 21-23 January 2014 in Bangkok, Thailand.  As a part of the conference EU BON is  going to hold a workshop called "Integration of biodiversity data recording and information management systems for environmental sustainability: a call for EU-ASEAN collaboration" (22nd January).

The agenda of the EU BON workshop includes:

• Review and compare the situation regarding relevant biodiversity and Earth observation data and information sources/providers in EU and ASEAN;

• Examine linkages between regional/national ASEAN and EU efforts with international / global biodiversity information systems (in particular GBIF, GEO BON);

• Assess and discuss national vs. regional level priorities and needs with regard to integrated biodiversity information in ASEAN and Europe;

• Identify common challenges and needs towards further integration of different types, levels, and scopes of available data and information systems;

• To address how S&T cooperation between Europe and ASEAN in the area of biodiversity and Earth observation could be further developed to better serve policy needs (especially in light of IPBES), and to contribute to common goals towards sustainable economic development

The ASEAN-EU Science, Technology and Innovation Days serve as a visible forum for cooperation activities between the two regions in the field of STI. The event addresses researchers from most thematic areas – with a focus on the societal challenges with relevance to both regions – as well policy makers, research conducting companies and innovation managers. It takes place annually, alternating between an ASEAN and a European country. High-level policy makers as well as many research projects and companies seize the chance to network, discuss, exchange and inform themselves.

The FP7 CLIMSAVE project ("Climate Change Integrated Assessment Methodology for Cross-Sectoral Adaptation and Vulnerability in Europe") finished at the end of 2013. The project developed the CLIMSAVE Integrated Assessment Platform which is a unique user-friendly, interactive web-based tool that enables stakeholders to interactively explore the complex multi-sectoral issues surrounding impacts, adaptation and vulnerability to climate and socio-economic change within the agriculture, forest, biodiversity, coast, water and urban sectors.  Two versions of the tool have been developed: one for Europe and one for Scotland.

On 19 Nov 2013, a one-day EU BON workshop took place at the Leibniz-Association Headquarter in Berlin to further develop the strategy for citizen science in the project.  The workshop was a joint workshop of both work package 1 and work package 6 (organized by MfN and UTARTU) to bring together the partners from EU BON that work in the area of citizen science. Furthermore, the workshop aimed to discuss and plan the further activities regarding the next stakeholder roundtable on Citizen Science which is scheduled for 2014.

In the morning session, participants gave an overview of citizen science activities within Europe. Eight presentations from partners gave insight into citizen science initiatives and showed interesting approaches of how citizens can be involved and how datasets with information on biodiversity can be generated (please find the pdf of the presentations and minutes of the meeting below). Linda Davies, director and initiator of OPAL, one of the Europe’s most well-known citizen science initiatives, encouraged to emphasize not just data-value of citizen science, but to look for educational and awareness-rising aspects.

After an informative session there were discussions how to proceed with citizen science related tasks in EU BON. The workgroup was formed to take next steps for developing the concept of a European citizen science strategy within EU BON. It was decided that best practice examples will be used to outline the most efficient methods for incorporating citizen science in biodiversity research. Many other next steps were discussed for EU BON’s citizen science initiative (definition of the concrete role EU BON can and should play, technical solutions for citizen science data and projects, further involvement of Citizen Science stakeholders, identification of gaps).

EU BON will further intensify the dialogue between different groups related to citizen science, after a big step was done by this meeting. For example, in the next EU BON stakeholder roundtable, stakeholders such as the EEA, DG Research and Communication, ECSA, Eye on Earth and other users from political administration and scientists will be involved to discuss their needs and the contribution EU BON may provide.

For further questions please contact Katrin Vohland or Veljo Runnel

Presentations from the meeting:

Cristina Garilao - FishWatcher

Falko Glöckler - Anymals and Plants

Katrin Vohland - Citizen Science Germany

Katrin Vohland - Preparation of citizen science stakeholder meeting

Thanos Dailianis - Greece SC Project COMBER

Veljo Runnel - CS in EU BON

Veljo Runnel - CS Science in Estonia

Wouter Koch - Norway CS Project Artsobservasjoner

Israel Peer - CS Status in Israel - GlueCAD

Minutes of the Meeting - Citizen Science Workshop

Pollination and Land Degradation: Set as top Priorities for New Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) after the plenary

IPBES was established in April 2012, as an independent intergovernmental body open to all member countries of the United Nations. The members are committed to building IPBES as the leading intergovernmental body for assessing the state of the planet's biodiversity, its ecosystems, and the essential services they provide to society.

The second meeting of the Platform's Plenary (IPBES-2) took place in Antalya, Turkey, from 9 to 14 December 2013. Around 400 delegates from over 100 governments, scientific organizations, civil society and the private sector, attended the plenary. It was agreed to develop a set of assessments on pollination and food production, land degradation and invasive species aimed at providing policymakers with the tools to tackle pressing environmental challenges.

IPBES Member Governments present at the meeting adopted a very ambitious initial work programme for the Platform for the next five years, and demonstrated strong commitment to its implementation by already pledging more than half (US$ 25.4 million) of the total US$ 43.5 million required, in what will be remembered as the "Antalya consensus".

EU BON was represented by the project coordinator Christoph Häuser (Museum für Naturkunde, MfN), and colleagues Tim Hirsch (Danish Biodiversity information Facility, DanBIF), Dirk Schmeller (Helmholtz Centre for Environmental Research, UFZ), Wolfgang Cramer and Ilse Geijzendorffer (National Center for Scientific Research, CNRS), Matthew Walpole (World Conservation Monitoring Centre, UNEP) and Lluís Brotons (European Bird Census Council, EBCC).

EU BON group photo from left to right: Tim Hirsch (DanBIF), Christoph Häuser (MfN), Matthew Walpole (UNEP), Ilse Geijzendorffer (CNRS), Dirk Schmeller (UFZ), Wolfgang Cramer (CNRS) and Lucas Joppa (Microsoft Reseach). Photo: Dirk Schmeller

Here are their views and comments on the meeting:

1) How can EU BON contribute to the success of IPBES?

Matthew Walpole: Knowledge generation is a key pillar of IPBES. Mobilising data and information on biodiversity and ecosystem services is an important element of knowledge generation, and will be vital in underpinning rigorous, comprehensive assessments. In that regard, and in particular in the context of potential European regional assessments, EU BON as an integral part of GEO BON has a clear contribution to make.

Dirk S. Schmeller: IPBES assessments will base on available data and newly collected data from organisations contributing to IPBES. While there are some global biodiversity information providers, like GBIF, EU BON goes further in bridging data collection and data infrastructure and transforming the data in policy relevant reports. Much of the work by IPBES relies on such a system, and EU BON would be a major step forward and if put on a global scale (as a contribution to GEO BON) will be crucial for the work of IPBES. EU BON should aim to organise a side event at IPBES-3, maybe jointly with GEO BON.

Tim Hirsch: EU BON and all of its partners, including GBIF, have a vitally important role in providing the data and information foundations for the work IPBES will carry out to strengthen the science-policy interface. All through the IPBES process, countries have committed to build on existing initiatives, and it is encouraging to see that approach is being followed as the institutions of the new platform emerge. For example, the proposed IPBES task force on knowledge and data, based on strategic partnerships with relevant institutions, provides a space for our data mobilization and integration activities  to contribute to the assessment, knowledge generation, capacity building and policy support functions of the platform.

Ilse Geijzendorffer: By giving them the knowledge of what is required for successful assessment execution in terms of infrastructure, data management and governance. We can also provide demo results for them, for instance by computing an indicator required in one of the required assessments. Then they can start thinking of how they would like to communicate about these kinds of results and put in place the necessary procedures. We could also offer our services for a case study with a developing country on one of the identified assessments to show how their data and experts (including local and indigenous knowledge holders) could be included in the assessment.

Christoph Häuser: Yes, EU BON can and most certainly will significantly contribute to IPBES: Regardless of what the first thematic priorities for IPBES assessments and reviews will be , all assessments will ultimately depend on available, reliable and meaningful biodiversity data and information. Here, EU BON will be able to help by showing new and practical ways how to access integrated data layers and sources at various scales and for different interest and purposes. EU BON will also be able to help IPBES with its large and growing networks of institutions and experts, ranging from technical to socio-political areas.

2) How can IPBES participants best be made aware of EU BON and its relevance for IPBES?

Lluis Brotons: First of all, IPBES is a global, really ambitious initiative and EU BON faces a real challenge to effectively reach the audience currently developing the platform. EU BON should carefully select bridging channels between the work developed within the project and the IPBES priorities. Once these priorities have been identified, EU BON could easily become a key partner in providing valuable information, methods and concepts to be used in the IPBES assessments. It will be specially important to focus on the thematic assessments that IPBES plans to carry out in the first place such as pollination and food production or the methodological oriented assessment on support tools and methodologies for scenario analysis and modelling of biodiversity and ecosystem services that should be started during 2014. The main work ahead for EU BON on  making IPBES participants best aware of our work rests upon our ability to translate EU BON facilities, data and methods to the approaches and needs of the platform. We will need to be proactive here, we should not wait for IPBES to ask for help, we need to offer it in an attractive and adequate manner.

Matthew Walpole: Whilst GEO BON will be known to participants, and is mentioned in IPBES documentation, EU BON as a contributor to GEO BON is currently less visible. It's profile may be best raised in the context of GEO BON's role, with particular reference to its unique contributions, including (i) in a European context as (ii) a potential model for other regions.

Dirk S. Schmeller: One important possibility to make EU BON more visible is to show what the BON could look like, what possibilities in regard to reporting tools exist and how it could contribute to GEO BON.

Tim Hirsch: It will be important for EU BON and its partners to continue to engage actively in the various processes and procedures that are emerging from this plenary meeting: for example where we may contribute data and information to the various thematic and regional assessments of biodiversity and ecosystem services that will be carried out during the first IPBES Work Programme over the next five years.

Christoph Häuser: While IPBES is still struggling to become really operational, EU BON should strive to lead by example: it could provide concrete show cases of integrative approaches towards biodiversity information; for example, how to pull together data from different layers, such as GBIF point occurrence and habitat or land cover data for a given areas, or how to operationalise Essential Biodiversity Variables or meaningful indicators from existing data sources.
 

3) Which IPBES members/participants/stakeholders do you see as key partners for EU BON, and which ones have you contacted?

Lluis Brotons: IPBES is still shaping itself and one of the challenges ahead for the platform is the participation of stakeholders in the different processes required to complete and analyse the planned thematic assessments.  In this line, in the second IPBES plenary, different EU BON partners have been teaming up with a number of other international stakeholders (IUCN, ICSU amongst others) to ensure that the scientific community and other knowledge holders directly contribute to the key parts of process. This is essential for the credibility of the assessments and the discussions in the meetings in Turkey have strongly revolved around the forms this participation may finally take. I would stress at this point that I do not clearly see key partners in IPBES, but more of a need to be also here proactive and work with other proactive stakeholders to articulate mechanisms by which non-governmental organisations are able to feed into the process. These mechanisms are likely to be critical in the future work of EU BON.

Matthew Walpole: There are various networks, initiatives and organisations promoting better biodiversity/environmental data mobilisation, integration, management and use (such as 'Eye on Earth' convened by the Abu Dhabi Global Environmental Data Initiative (AGEDI)). GEO BON/EU BON members (including GBIF and UNEP-WCMC) participate in such networks and it would be beneficial to forge stronger collaborative links. Other obvious partners include regional/national biodiversity centres beyond Europe with which EU BON might share/compare approaches as part of regional exchange and capacity development.

Tim Hirsch: It will particularly important to engage with the members of the Multidisciplinary Expert Panel (MEP) elected from each region to guide the scientific priorities of the platform's work, based on requests from governments, as well as the many scientific bodies, civil society groups and of course governments involved in the new platform - I have contacted a good proportion of them!

Ilse Geijzendorffer: Firstly, the stakeholder representation (our infrastructure could be included in the end as in kind contribution by an institute or network). Secondly, delegates favourable of scientific IPBES involvement (e.g. Switzerland, Germany, Portugal, the Netherlands, and Germany). I have not talked to Switzerland and the Netherlands.

Christoph Häuser: During IPBES2, I had the opportunity to make contacts with NatureServe, a prime organization and big player focusing on biodiversity information in the Western Hemisphere. It is these kinds of regional or global organizations with significant experiences and substantial assets in the area of biodiversity information generation and management, which EU BON should be liaising with more. With the (current) IPBES plenary being very much dominated by governments, it will remain a good forum for scientific initiatives and projects, such as EU BON, to build links to the political level, practically from all regions.

Dirk S. Schmeller: I agree with Christoph that EU BON needs to identify key players, such as Nature Serve, Earth Watch, dataONE and others. I had the pleasure to talk to the lead scientist of Nature Serve here in Antalya, Healy Hamilton, who expressed her interest in EU BON and GEO BON to allow an exchange of experiences and technologies. Such a collaboration will likely be beneficial for both projects/organisations. My interactions with MEP members from the different UN regions as well as delegates from different countries, which were much facilitated by IPBES, also did show the huge interest of these peers in an observation system to inform policy, but also the gaps in making known EU BON and GEO BON in some regions (e.g. Caribbean were unaware of GEO BON).

4) Which will be the emerging/new areas/challenges/questions regarding biodiversity data and monitoring coming from IPBES which EU BON needs to consider / take on board?

Lluis Brotons: Since IPBES it is in its early stages it is still difficult to identify specific questions or challenges regarding biodiversity data needs for this process. However, the advice I can give to EU BON partners is that they become familiar as early as possible with the scoping of the thematic assessments planned within the context of IPBES in the forthcoming years. The information provided in the initial scoping of these assessments may be a useful tool for EU BON allowing the different groups to move their developments in line that anticipate the needs that the assessments are likely to face in the near future. Explore the scoping for the thematic assessments (amongst other IPBES documents) here (http://ipbes.net/plenary/ipbes-2-documents.html)

Matthew Walpole: EU BON could usefully consider and articulate which parts of the IPBES conceptual framework it can provide information for, as well as thinking about how it connects to regional (European), and global, assessment processes within the IPBES programme of work. Equally, given the importance within IPBES placed upon outreach and communication to decision-makers across multiple sectors, EU BON could usefully consider innovative visualisation approaches for its data products and outputs.

Tim Hirsch: One of the strong themes that has run through this IPBES meeting is the need to incorporate and recognize multiple knowledge systems, including indigenous and traditional knowledge, when carrying out assessments of biodiversity and ecosystem services. There are many challenges and opportunities arising out of this for EU BON and its partners, for example the development of community-based monitoring programmes that can contribute valuable data and information for the science-policy interface, but must be handled with due respect and sensitivity to build trust in participating communities.

Ilse Geijzendorffer: Fast track assessments, need their answers fast! Additionally, transparency of the analysis maybe not appreciated by some regional hubs or Members of the platform. This maybe posing problems for the willingness to use a shared data transfer system. Finally, if 80% of the experts will be nominated by the Members of the Platform, this can pose problems for the willingness of some expert to use transparent analysis methods. This has to be endorsed in the current protocol development.

Christoph Häuser: This remains a largely open question, as IPBES is still much preoccupied with procedural and organizational issues. With the regional approach towards assessments built into IPBES, however, it is already clear that a regional perspective towards biodiversity information and interpretation, such as an integrated European biodiversity data portal, will be a major asset to offer. As IPBES furthermore stresses the incorporation of other forms of knowledge, a focus on linking with and incorporating citizen science initiatives seems a logical follow up for EU BON.

Today, 16/12/2013,  the European Commission announced the launch of a new Pilot on Open Research Data in Horizon 2020, to ensure that valuable information produced by researchers in many EU-funded projects will be shared freely. Researchers in projects participating in the pilot are asked to make the underlying data needed to validate the results presented in scientific publications and other scientific information available for use by other researchers, innovative industries and citizens. This will lead to better and more efficient science and improved transparency for citizens and society. It will also contribute to economic growth through open innovation. For 2014-2015, topic areas participating in the Open Research Data Pilot will receive funding of around €3 billion.

The Commission recognises that research data is as important as publications. It therefore announced in 2012 that it would experiment with open access to research data (see IP/12/790). The Pilot on Open Research Data in Horizon 2020 does for scientific information what the Open Data Strategy does for public sector information: it aims to improve and maximise access to and re-use of research data generated by projects for the benefit of society and the economy.

The Pilot involves key areas of Horizon 2020:

• Future and Emerging Technologies

• Research infrastructures – part e-Infrastructures

• Leadership in enabling and industrial technologies – Information and Communication Technologies

• Societal Challenge: Secure, Clean and Efficient Energy – part Smart cities and communities

• Societal Challenge: Climate Action, Environment, Resource Efficiency and Raw materials – with the exception of topics in the area of raw materials

• Societal Challenge: Europe in a changing world – inclusive, innovative and reflective Societies

• Science with and for Society

Neelie Kroes, Vice-President of the European Commission for the Digital Agenda said "We know that sharing and re-using research data holds huge potential for science, society and the economy. This Pilot is an opportunity to see how different disciplines share data in practice and to understand remaining obstacles."

Commissioner Máire Geoghegan-Quinn said: "This pilot is part of our commitment to openness in Horizon 2020. I look forward to seeing the first results, which will be used to help set the course for the future."

Projects may opt out of the pilot to allow for the protection of intellectual property or personal data; in view of security concerns; or should the main objective of their research be compromised by making data openly accessible.

The Pilot will give the Commission a better understanding of what supporting infrastructure is needed and of the impact of limiting factors such as security, privacy or data protection or other reasons for projects opting out of sharing. It will also contribute insights in how best to create incentives for researchers to manage and share their research data.

The Pilot will be monitored throughout Horizon 2020 with a view to developing future Commission policy and EU research funding programmes.

The 2013 International Conference on Open Data in Biodiversity and Ecological Research took place between 20 - 22 Nov 2013, hosted by Academia Sinica in Taipei, Taiwan. With the aim to promote open data in science twelve foreign speakers introduced relevant projects and initiatives in the sphere of biodiversity informatics: AP-BON, DataONE, Ecological Research, EU-BON, Global Biodiversity Information Facility (GBIF), Japan Biodiversity Information Facility (JBIF), linked open data, National Ecological Observatory Network (NEON), Pensoft, and Thomson Reuters.

Dirk Schmeller (UFZ) and Lyubomir Penev (Pensoft), who presented EU BON at the conference, share their experience in a recent interview:

What are the aims and main outcomes from this meeting?

LP: Taiwan has an impressive national policy with regard to data management in biodiversity sciences. The meeting summarised years of effort of Taiwanese scientists and especially of Academia Sinica to integrate data and make them publicly available. It is sufficient to mention that Taiwan has established four national nodes of the largest international biodiversity platforms, that is TaiBIF (of GBIF), TaiCOL (of Catalogue of Lige), TaiEOL (of EOL) and TaiBOL (of Barcode of Life).

Were there any biodiversity data integration models presented at the meeting that can be adopted and implemented in EUBON?

LP: Perhaps not directly, however the impressive amount and quality of work and the accumulated experience of the Taiwanese and Japanese colleagues would certainly be of value for EU BON. In addition, there are well established contacts already between the FP7 project SCALES and the National University of Taiwan which could serve as a stepping stone as well, because two of the SCALES partners participate in EU BON and at the meeting (UFZ and Pensoft).

The interest to the EU BON presentation by Dirk was great. An indicator for that was that more  than 120  EU BON leaflets have been picked up by the participants from the information desk.

Did you discuss any opportunities for partnership with organizations and initiatives from Asia and America, which deal with biodiversity data integration and accessibility?

LP: Yes, there were a lot of discussions how to mobilize and publish biodiversity data and most probably several data publishing projects will appear as a result of the discussions. These pilots could be used for the EU BON goals.

US National Ecological Observatory Network (NEON) has activities similar to those planned by WP4 Link environment to biodiversity: analyses of patterns, processes and trends. Is there something that EU BON can learn from the experience of its American colleagues?

DS: It is important to keep a close link with Brian Wee and NEON, as they have a head start in comparison to EU BON. I am sure that a collaboration would benefit EU BON to work efficiently.

What is your prognosis for the successful establishment of the data publishing model in scholarly literature, and more specifically in spheres such as Ecology, Genetics, Physiology and Paleontology?

DS: Most research is financed by taxpayer money and should become publicly available once the analyses a researchers has intended are completed. I see a huge potential to publish this data in scholarly literature. I, however, see also quite some difficulties to recombine relevant datasets across different sources for further going analyses. I also see difficulties in the willingness of researchers to share data, as in many cases they see these as their own.

Linked Open Data (LOD) is a new and prominent technology to publish and share data on the web. Could you please explain what exactly hides behind this concept, and how could EU BON benefit from it?

LP: The meeting in Taiwan was impressive also in the wide representation of the Resource Description Framework (RDF) technologies in integration of biodiversity data, especially from a group from the National Museum of Japan and the University of Tokyo. RDF and the OWL Web Ontology Language are definitely the way to go if we want to make diverse data sets interoperable; the implementation of RDF in a pilot phase would be of primary importance for the success of EU BON.

Ecological modellers require reliable sources of data for their analysis. Often, these sources are databases, checklists and specimen labels. Yet another rich source is the corpus of biological literature. It is estimated that there are well over 100 million pages of scientific publications and the volume grows every year. Publishing in advanced XML-based journals, such as Zookeys, Phytokeys or the Biodiversity Data Journal is recommended for new data, but what is the solution for legacy texts?

The EU FP7 project pro-iBiosphere has been piloting the mark-up and extraction of biological information from literature, which has been pioneered by Plazi (Agosti & Egloff, 2009). The EU FP7 Coordination and Support Action "pro-iBiosphere" was launched to investigate ways to increase the accessibility of biodiversity data, improve the efficiency of its curation and increase the user base of biodiversity data consumers and applications. The project addresses the technical and semantic interoperability between different forms in which data are published and analyses the sustainability issues related to the maintenance and curation of biodiversity data and derived information and knowledge. It also involves encouraging the biodiversity community to publish biodiversity data in a way that satisfies the technical requirements for an envisioned Open Biodiversity Knowledge Management System.

In order to reach these objectives three pilots for data mark-up and one for interoperability are being conducted (for detailed information on the pilots please see here). The mark-up pilots are evaluating accessibility of data within literature for a wide range of organisms and data types; and ways to facilitate  extraction of biological information from literature, including observations, traits, nomenclature, habitat information and interactions between organisms. For example, one pilot is looking at biogeographic data using the species Chenopodium vulvaria as a subject. In another, trait data is being extracted from literature on tropical mistletoes; while yet others are extracting data from papers on spiders, ants, centipedes, mosses and fungi.

In order to extract these data one can use either "born" digital texts or scanned texts, converted through text capture. These texts are then progressively marked up into XML documents, with tags defining the meaning of the containing text. The degree of mark-up granularity and the choice of textual elements to be marked-up depend on the type of data to be extracted and its granularity in the text. In taxonomically based literature, text is usually divided into the individual "treatments" for each species. Fortunately, most paragraph elements of these texts are in standard formats, for example, separate blocks of text contain the physical description of the organism, details of the distribution and habitat information, often separated with sub-headings.

The pro-iBiosphere pilots have used several methods for mark-up, but the main tool has been the GoldenGate Editor, which combines manual and automated methods to identify key text elements. For example, an algorithm identifies Latin names and then an interface guides the user through the verification of the algorithm’s results. Once marked-up, the XML document can be uploaded to the Plazi document repository. Plazi is a not-for-profit organization devoted to promoting open-access to taxonomic literature. You are free to use the data contained in Plazi’s repository and if you want you can refine the mark-up for your own purposes.

Extracting data from the legacy literature can be expensive. Modern XML based publications have additional advantages of linkages via DOI identifiers, and immediate dissemination to harvesters like EOL or GBIF. Yet, digitisation and mark-up has the possibility to reanimate the data in our publications, making them almost as useful as modern linked publications.

Task 3.4 of EU-BON is to develop tools to prepare, extract and mine published biodiversity literature (led by Plazi - Donat Agosti). For this task Plazi is looking for rich sources of data from the biodiversity literature, particularly where those data can be applied within other EU-BON tasks. For further information please contact Plazi

Agosti, D., & Egloff, W. (2009). Taxonomic information exchange and copyright: the Plazi approach. BMC research notes, 2(1), 53. doi:10.1186/1756-0500-2-53

Quentin Groom (National Botanic Garden, Belgium) & Donat Agosti (Plazi)

The Martin-Luther-Universität Halle-Wittenberg offers in cooperation with GEO BON and iDiv the position of Executive Director for the duration of 30 months (initially limited till September 30th, 2016 with possibility of extension). The Executive Director will work in close collaboration with the incoming Chair of the GEO BON Steering Committee, Prof. Henrique M. Pereira (iDiv) and the incoming vice-chair, Dr. Mike Gill (Environment Canada), thematic workgroup coordinators, regional BON coordinators, the GEO BON Steering Committee and the GEO secretariat.

Requirements:
• Ph.D. in ecology or related field
• excellent diploma or master degree in a relevant field
• demonstrable experience in project management with executive leadership in organizations a plus
• excellent communication skills, fluency in English, knowledge of other languages being a plus
• willingness to travel abroad frequently, outgoing and at ease in multicultural backgrounds

Topic/job description:
• Providing visible leadership for GEO BON and representing GEO BON at scientific and policy meetings
• Creating funding opportunities through engagement with potential donors
• Coordinating activities of GEO BON Working Groups and Regional Observation Networks
• Liaising with national and regional organizations involved in biodiversity monitoring and reporting
• Organize the Steering Committee, All-hands and other meetings of GEO BON and manage the communication activities of GEO BON, including a regular newsletter and a website
• Manage, as and when required, activities and inputs requested by the GEO secretariat

Applications should be directed to emily.keller@idiv.de and addressed to Henrique M. Pereira, Professor of Biodiversity Conservation, iDiv. Applications should be in a single PDF file with reference file number (D 189/2013). Applications are accepted until January 6th, 2014.

For more information see attached the full text of the job offer.

The final EUBrazilOpenBio newsletter for November 2013 is now available. The  newsletter presents the final press release showcasing the main results of 2 year collaborative work, namely: the innovative, web-based working environment designed to serve biodiversity scenarios; the new version of the Catalogue of Life cross-mapping tool developed in the i4Life project; the provision of the Ecological Niche Modelling tool as a service through the openModeller extended web service, and its application in collaboration with BioVeL; the EUBrazilOpenBio Joint Action Plan.

This newsletter highlights:

• EUBrazilOpenBio Joint Action Plan - drawing on policy strategies, analysing  current progress in contributing to international targets and defining actions for future collaborative research. It defines common actions with the aim of contributing to relevant Aichi Targets in the years ahead.
• EGI federatec use case on ecology - Over the last two years, BioVeL and EUBrazilOpenBio have joined forces to make openModeller ready for cloud deployment. Work within the EGI Federated Cloud Task Force has led to considerable success in enabling the openModeller service on the EGI Federated Cloud.
• EUBrazilOpenBio results - EUBrazilOpenBio Technical developments, training materials and sessions, publications and papers, media spotlights and policy results all collected in one page.
• A vision from the Experts - "The Crossmapper itself is a great tool, and an ideal way to identify errors and updates". Dr Christina Flann is one of the experts providing their vision on EUBrazilOpenBio story.

You can find an online version of the final EUBrazilOpenBio newsletter here.

The Environmental Change Institute (ECI) in the University of Oxford is seeking to appoint a Postdoctoral Research Assistant to join the existing research team on two EU funded research projects: IMPRESSIONS and OPENNESS.

The role will require the development of a range of methodological and modelling approaches, including quantitative, qualitative and mixed techniques, to address a number of environmental science challenges in the contexts of operationalising ecosystem services and investigating cross-sectoral climate change impacts and vulnerabilities. The post provides the opportunity for a researcher with skills in programming, GIS and statistics to develop innovative solutions in research areas critical to ensuring the resilience of our future environment and to expand the modelling capability of the ECI team.

You will have a PhD in a discipline relevant to modelling or environmental sciences and a background in programming and modelling. You will have experience of using Geographical Information Systems and a strong grounding in statistics and/or operational research. Excellent communication skills both written and oral are essential. You will be self-motivated, with the ability to work independently.

This post is available for 24 months in the first instance.

The closing date for applications is 12.00 noon on Wednesday 18 December 2013. It is intended that interviews will be held during the week beginning 13 January 2014.

For more information and to apply for this position, click here.

The Environmental Change Institute (ECI) in the University of Oxford is seeking to appoint a Research Assistant to join the existing research team on two EU funded research projects.

The role will require the development and application of methodologies for undertaking systematic literature reviews, quantitative analysis of model outputs, contribution to the writing of research papers, organisation of workshops and large meetings, and the performance of other duties necessary for the successful completion of both the IMPRESSIONS and OPENNESS projects

You will have a Masters or equivalent in an environmental discipline and strong quantitative skills. You must have the ability to undertake systematic literature reviews and synthesise findings and assist in the management of large research projects. Excellent organisational and writing skills are essential.

This is a part-time (50% FTE) post and is available for 24 months.

The closing date for applications is 12.00 noon on Wednesday 18 December 2013.

You can find more information and apply here.

The latest issue of ZooKeys - no. 346 - has been automatically registered in ZooBank on its day of publication last Friday. This marks the successful deployment of an automated registration-to-publication pipeline for taxonomic names for animals. The innovative workflow was jointly funded by the EU FP7 funded project pro-iBiosphere and a U.S. National Science Foundation project to develop the Global Names Architecture (DBI-1062441).

The process of post-publication recording and indexing of species names has a long tradition, in some cases dating as far back as the middle of 19th century. But now in the 21st century with the advance of modern technologies and the opportunity to publish taxonomic novelties online, the process of post-publication recording brought into focus the concept of automated pre-publication registration.

Why is this important? The proportion of 'turbo-taxonomic' papers describing hundreds of new species increases. Registration of hundreds of new species is an issue, however it is even more important that the final publication data of the pre-registered names are reported back to ZooBank on the day of publication.

Launched as an open access peer reviewed journal in 2008, to coincide and adopt from inception the International Code of Zoological Nomenclature changes for electronic publications, ZooKeys was the first journal to provide a mandatory in-house registration in ZooBank. Since 2008, it has contributed about one third of all names currently registered in ZooBank. With the adoption of the automated ZooBank registration, ZooKeys continues its mission to set novel trends in biodiversity publishing.

Implementation of automated workflows and invention of XML-based tools will facilitate the process of publication and dissemination of biodiversity information. It will pave the way for unification and streamlining the registration process, even more to building the next-generation e-infrastructure for a common global taxon names registry. Within the pro-iBiosphere project and in cooperation with Plazi that have created the TaxPub XML schema, an automated registration workflow for plants has already been established between the International Plant Names Index (IPNI) and the PhytoKeys journal, to be applied soon also for fungi between Index Fungorum and the journal MycoKeys.

By http://www.eea.europa.eu/

Grassland butterflies have declined dramatically between 1990 and 2011. This has been caused by intensifying agriculture and a failure to properly manage grassland ecosystems, according to a report from the European Environment Agency (EEA).

Taxonomic descriptions, introduced by Linnaeus in 1735, are designed to allow scientists to tell one species from another. Now there is a new futuristic method for describing new species that goes far beyond the tradition. The new approach combines several techniques, including next generation molecular methods, barcoding, and novel computing and imaging technologies, that will test the model for big data collection, storage and management in biology. The study has just been published in the Biodiversity Data Journal.

While 13,494 new animal species were discovered by taxonomists in 2012, animal diversity on the planet continues to decline with unprecedented speed. Concerned with the rapid disappearance rates scientists have been forced towards a so called 'turbo taxonomy' approach, where rapid species description is needed to manage conservation.

While acknowledging the necessity of fast descriptions, the authors of the new study present the other 'extreme' for taxonomic description: "a new species of the future". An international team of scientists from Bulgaria, Croatia, China, UK, Denmark, France, Italy, Greece and Germany illustrated a holistic approach to the description of the new cave dwelling centipede species Eupolybothrus cavernicolus, recently discovered in a remote karst region of Croatia. The project was a collaboration between GigaScience, China National GeneBank, BGI-Shenzhen and Pensoft Publishers.

Eupolybothrus cavernicolus has become the first eukaryotic species for which, in addition to the traditional morphological description, scientists have provided a transcriptomic profile, DNA barcoding data, detailed anatomical X-ray microtomography (micro-CT), and a movie of the living specimen to document important traits of its behaviour. By employing micro-CT scanning in a new species, for the first time a high-resolution morphological and anatomical dataset is created - the 'cybertype' giving everyone virtual access to the specimen.

This, most data-rich species description, represents also the first biodiversity project that joins the ISA (Investigation-Study-Assay) Commons, that is an approach created by the genomic and molecular biology communities to store and describe different data types collected in the course of a multidisciplinary study.

"Communicating the results of next generation sequencing effectively requires the next generation of data publishing" says Prof. Lyubomir Penev, Managing director of Pensoft Publishers. "It is not sufficient just to collect 'big' data. The real challenge comes at the point when data should be managed, stored, handled, peer-reviewed, published and distributed in a way that allows for re-use in the coming big data world", concluded Prof. Penev.

"Next generation sequencing is moving beyond piecing together a species genetic blueprint to areas such as biodiversity research, with mass collections of species in "metabarcoding" surveys bringing genomics, monitoring of ecosystems and species-discovery closer together. This example attempts to integrate data from these different sources, and through curation in BGI and GigaScience's GigaDB database to make it interoperable and much more usable," says Dr Scott Edmunds from BGI and Executive Editor of GigaScience.

Additional information:

Pensoft and the Natural History Museum London have received financial support by the EU FP7 projects ViBRANT and pro-iBiosphere. The China National GeneBank (CNGB) and GigaScience teams have received support from the BGI. The DNA barcodes were obtained through the International Barcode of Life Project supported by grants from NSERC and from the government of Canada through Genome Canada and the Ontario Genomics Institute.

Original Sources:

Stoev P, Komerički A, Akkari N, Shanlin Liu, Xin Zhou, Weigand AM, Hostens J, Hunter CI, Edmunds SC, Porco D, Zapparoli M, Georgiev T, Mietchen D, Roberts D, Faulwetter S, Smith V, Penev L (2013) Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodiversity Data Journal 1: e1013. DOI: 10.3897/BDJ.1.e1013

Edmunds SC, Hunter CI, Smith V, Stoev P, Penev L (2013) Biodiversity research in the "big data" era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2:14 doi:10.1186/2047-217X-2-14

Watch the 3D cybertype video: http://www.youtube.com/watch?v=vqPuwKG8hE4&feature=em-upload_owner

The Biodiversity Data Journal goes beyond the basics of the Gold Open Access

There are two main modes of open access publishing – Green Open Access, where the author has the right to provide free access to the article outside the publisher's web site in a repository or on his/her own website, and Gold Open Access, where articles are available for free download directly from the publisher on the day of publication.

Opening of content and data, however does not necessarily mean "easy to discover and re-use". The Biodiversity Data Journal proposed the term "Advanced Open Access" to describe an integrated, narrative (text) and data publishing model where the main goal is to make content "re-usable" and "interoperable" for both humans and computers.

To publish effectively in open access, it is not sufficient simply to provide PDF or HTML files online. It is crucial to put these under a reuse-friendly license and to implement technologies that allow machine-readable content and data to be harvested and collated into a big data pool.

The Advanced Open Access means:

• Free to read
• Free to re-use, revise, remix, redistribute
• Easy to discover and harvest
• Content automatically summarised by aggregators
• Data and narrative integrated to the widest extent possible
• Human- and computer-readable formats
• Community-based, pre- and post-publication peer-review
• Community ownership of data
• Free to publish or at low cost affordable by all

BDJ shortens the distance between "narrative" (text) and "data" publishing. Many data types, such as species occurrences, checklists, measurements and others, are converted into text from spreadsheets for better readability by humans. Conversely, text from an article can be downloaded as structured data or harvested by computers for further analysis.

"Open access is definitely one of the greatest steps in scientific communication comparable to the invention of the printing technology or the peer-review system. Great but not sufficient!" said Prof. Lyubomir Penev, founder of Pensoft Publishers and the Biodiversity Data Journal. "We need to switch the focus already from making content 'available for free download' to being discoverable and extractable. Such re-usability multiplies society's investment in science".

Additional information:

The Biodiversity Data Journal is designed by Pensoft Publishers and was funded in part by the European Union's Seventh Framework Program (FP7) project ViBRANT.

Source: Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: 10.3897/BDJ.1.e995

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. Through an agreement with the Belgian Development Cooperation and as part of the FishBase programme, the RMCA has five grants available for a 3-month training programme in the use of FishBase and the taxonomy of African fishes.

The training includes three subsets:

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

The main focus of the training is on fish biodiversity data and their integration into FishBase, and on how to use and contribute data to FishBase. The context of these contributions may vary and can also include the knowledge on common names, fish ecology, fisheries statistics, aquaculture and many other areas of fish biology.

After the training, the participants should be able to make their own contribution to fish biology and continue to work on FishBase. They are encouraged to teach their newly apprehended skills to new/local users, to help in completing the database and keeping it up to date, and to spread the use of FishBase as a source of information and a fisheries tool.

This course has been offered annually since 2005 and is held at the Royal Museum for Central Africa (Leuvensesteenweg 13, B-3080 Tervuren, Belgium).

To apply for traineeship and for more information, go to:
http://www.africamuseum.be/research/collaborations/training/group?set_language=en&cl=en

Please note that for 2014, this course will be given in French only.

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

A correspondence item, published today, 10 Oct 2013, in Nature focuses on the upcoming calls for Horizon 2020 research funding. The European Commission has said that it would prefer bids from open, collaborative consortia rather than the competitive bids seen in previous funding programmes. The authors call for an effort to forge interdisciplinary links in biodiversity research, and ask readers to contribute to discussions on project ideas.

For more information read the full correspondence item in Nature: http://www.nature.com/nature/journal/v502/n7470/full/502171d.html

The 2014 SCIENCE POLICY SYMPOSIUM to support the implementation of the 2020 Biodiversity strategy and the EU Water Framework Directive will be held between 29-30 Jan 2014 in the Museum of Natural Sciences (RBINS), Brussels. The symposium is jointly organised by the EU FP7 funded projects BioFresh and REFRESH.

Numerous EU biodiversity and water related policies have been designed to protect freshwater ecosystems and ensure their sustainable use. However, major challenges still persist in the implementation of these policies. Freshwater ecosystems support 10% of all animal species on Earth and provide a diverse array of functions and services that contribute to human well-being. In recent decades global freshwater biodiversity has declined at a greater rate compared to terrestrial and marine ecosystems.

The Science Policy Symposium for Freshwater Life is organised with the aim of bringing together policy makers and stakeholders from the water, energy and conservation sector, NGOs, the scientific community and selected experts to discuss challenges to implementing the 2020 Biodiversity strategy and the EU Water Framework Directive.

Contact: waterlives.commitee@freshwaterbiodiversity.eu

Global Biodiversity Informatics Outlook sets out key steps to harness IT and open data to inform better decisions

Copenhagen, Denmark – A new initiative launched today (2 Oct) aims to coordinate global efforts and funding to deliver the best possible information about life on Earth, and our impacts upon it.

The Global Biodiversity Informatics Outlook sets out a framework to harness the immense power of information technology and an open data culture to gather unprecedented evidence about biodiversity and to inform better decisions.

The framework is outlined in a document and website entitled Delivering Biodiversity Knowledge in the Information Age, inviting policy makers, funders, researchers, informatics specialists, data holders and others to unite around four key focus areas where progress is needed.

The focus areas, each consisting of several specific components, are:

• Culture – promoting practices and infrastructure for sharing data, using common standards and persistent archives, backed up by strong policy incentives and a community of willing specialists;
• Data – addressing the need to transform all data about species, past and present, into usable and accessible digital formats; from historic collections and literature to citizen science observations, remote sensors and gene sequencing;
• Evidence – organizing and assessing data from all sources to provide clear, consistent views giving them context; including taxonomic organization, integrated occurrences in time and space, capturing information about species interactions, and improving data quality through collaborative curation; and
• Understanding – building models from recorded measurements and observations to support data-driven research and evidence-based planning, including predictive tools, better visualization and feedbacks to prioritize new data capture.

The document is being promoted through a number of upcoming events this month, including the Governing Board of the Global Biodiversity Information Facility and the Subsidiary Body on Scientific, Technical and Technological Advice of the Convention on Biological Diversity (CBD SBSTTA) where it forms part of the discussion on meeting global targets to end biodiversity loss.

The framework arose from the Global Biodiversity Informatics Conference which gathered around 100 experts in Copenhagen in July, 2012, to identify critical questions relating to biodiversity and tools needed answer them. Workshop leaders at that conference went on to draw up and author the current document.

The Global Biodiversity Informatics Outlook includes examples of projects and initiatives contributing to its objectives, and the accompanying website www.biodiversityinformatics.org invites feedback from others wishing to align their own activities to the framework.

A deck of slides for presentations about GBIO is available at http://www.slideshare.net/GBIF/global-biodiversity-informatics-outlook

The Biodiversity Data Journal (BDJ) and the associated Pensoft Writing Tool (PWT), launched on 16th of September 2013, offer several innovations - some of them unique - at every stage of the publishing process. The workflow allows for authoring, peer-review and dissemination to take place within the same online, collaborative platform.

Open access to content and data is quickly becoming the prevailing model in academic publishing, resulting in part from changes to policies of governments and funding agencies and in part from scientist's desire to get their work more widely read and used. Open access benefits scientists with greater dissemination and citation of their work, and provides society as a whole access to the latest research.

To publish effectively in open access, it is not sufficient simply to provide PDF files online. It is crucial to put them under a reuse-friendly license and to implement technologies that allow machine-readable content and data to be harvested by computers that can collate small scattered data into a big pool. Analyses and modelling of community-owned big data are the only way to confront environmental challenges to society, such as climate change, ecosystems destruction, biodiversity loss and others.

Manuscripts are not submitted to BDJ in the usual way, as word processor files, but are written in the online, collaborative Pensoft Writing Tool (PWT), that provides a set of pre-defined, but flexible article templates. Authors may work on a manuscript and invite external contributors, such as mentors, potential reviewers, linguistic and copy editors, and colleagues, who may read and comment on the text before submission. When a manuscript is completed, it is submitted to the journal with a simple click of a button. The tool also allows automated import of manuscripts from data management platforms, such as Scratchpads.

"This is the first workflow ever to support the full life cycle of a manuscript, from initial drafting through submission, community peer-review, publication and dissemination within a single, online, collaborative platform. By publishing papers in all branches of biodiversity science, including novel article types, such as data papers and software descriptions, BDJ becomes a gateway for either large or small data into the emerging world of "big data", said Prof. Lyubomir Penev, managing director and founder of Pensoft Publishers.

BDJ shortens the distance between "narrative (text)" and "data" publishing. Many data types, such as species occurrences, checklists, measurements and others, are converted into text from spreadsheets into a human-readable format. Conversely text from an article can be downloaded as structured data or harvested by computers for further use.

A novel community-based peer-review provides the opportunity for a large number of specialists in the field to review a manuscript. Authors may also opt for an entirely public peer-review process. Reviewers may opt to be anonymous or to disclose their names. Editors no longer need to check different reviewers' and author's versions of a manuscript because all versions can be consolidated into a single online document, again at the click of a button.

"The Biodiversity Data Journal is not just a journal, not even a data journal in the conventional sense. It is a completely novel workflow and infrastructure to mobilise, review, publish, store, disseminate, make interoperable, collate and re-use data through the act of scholarly publishing!" concluded Dr Vincent Smith from the Natural History Museum in London, the journal's Editor-in-Chief.

The platform has been designed by Pensoft Publishers and was funded in part by the European Union's Seventh Framework Program (FP7) project ViBRANT.

Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: 10.3897/BDJ.1.e995

At the Bioinformatics Horizon 2013 Conference (3 - 6 September 2013, Rome) a Memorandum of Understanding was signed between PESI and EU BON. Christoph Häuser, on behalf of EU BON and Yde de Jong on behalf of PESI (see picture below), signed the document to strengthen the cooperation and formalise the integrating efforts of the European species infrastructures.  

PESI is now a new associate partner of EU BON, a consortium with currently 30 partners from 18 countries. One of the common aims of EU BON and PESI will be to establish and sustain standard taxonomies for Europe.  EU BON will support the PESI backbone developments, including its components, with a focus on Fauna Europaea and Euro+Med. Besides analyzing current gaps, new ideas will be developed to trigger expert involvement and enhance the data management systems.

In a side-meeting at BIH 2013, some ideas were discussed with available EU BON and PESI partners. Important steps will be taken to secure the sustainability of databases and expertise networks combined with the development of technical innovations for users and stakeholders and to promote the implementation of PESI as a European (INSPIRE) standard. It will be also important to further integrate the huge expertise networks, outreach to PESI Focal Points and expand the geographical scope. Furthermore, it will be important to integrate additional data types and data-resources.

ANNOUNCEMENT: The June 2013 update of the FishBase (www.fishbase.org) and SeaLifeBase (www.sealifebase.org/) websites are now available online.

FishBase Stats to date: 32500 Species, 299700 Common names, 52500 Pictures, 48700 References, 2010 Collaborators, 700000 Visits/Month

SealifeBase stats to date: 125800 Species, 27200 Common names, 11100 Pictures, 17800 References, 250 Collaborators

From 16^th to the 18^th of July, a European stakeholder consultation for the Intergovernmental Platform on Biodiversity & Ecosystem Services (IPBES) took place in Leipzig (Germany). The consultation was organized by three European Biodiversity Platforms: Network-Forum Biodiversity Research Germany (NeFo), the Belgian Biodiversity Platform, and the French Foundation for Research on Biodiversity (FRB) (further information on the conference: www.biodiversity.de/index.php/de/ipbes/nefo-aktivitaeten-zu-ipbes/workshops/pan-european-stakeholder-consultation).

IPBES will greatly influence future biodiversity policy and research, and EU BON is expected to provide a European contribution to IPBES. IPBES will be in particular of high interest, because it will need tools to integrate and analyse different data sources, to develop relevant infrastructure and to do assessments of state and trends of biodiversity at multiple scales.

EU BON was represented by several partners at the meeting and we acted as facilitators in the round-tables, gathered input for the project, participated in discussions and exchanged ideas with many representatives and colleagues. We provide you with a short summary of the meeting below.

The aims of the pan-European stakeholder consultation meeting in Leipzig were:

1. To reach out to stakeholders to inform people and institutes and to raise awareness of the dynamics in IPBES.
2. To discuss and obtain feedback on several IPBES-related documents that are currently being drafted. In their final form these documents will be submitted to the Panel for the IPBES 2 plenary session in 9-14 December 2013.

The meeting in Leipzig was organized around round table discussions of several draft documents of importance for stakeholders: the draft work programme, the stakeholder engagement strategy draft and the draft "Vision for pan-European IPBES support perspective". If you are interested these documents, currently for review, can be found here:  http://www.ipbes.net/intersessional-process/current-review-documents-ipbes2.html .

There were several opportunities for EU BON partners to flag the potential biodiversity data and analysis requirements for the future IPBES work program in separate discussions and to give recommendations as to what should be additionally integrated in the draft work programme.

We also brainstormed on a potential EU BON side event at the second IPBES meeting, which will be held in 9-14 December in Antalya, Turkey. Topics discussed by national delegates in that plenary will amongst other topics comprise: the first work programme, budget, stakeholder engagement, the position of observers, technical requirements and a list of thematic priorities for IPBES assessments.

Although the meeting was a success in terms of the number and diversity of participants, the consultation felt for many participants as a top down exercise. However, the importance of being involved at this stage was felt and the hope for stakeholder empowerment in the future was often voiced.

In 2013, the University of Potsdam will host the 43rd Annual Meeting of the Ecological Society of Germany, Austria and Switzerland. The meeting (www.gfoe-2013.de) will take place from September 9 to 13, 2013 in Potsdam, Germany.

The guiding theme of the 43rd Annual Meeting is "Building bridges in ecology - linking systems, scales and disciplines".
Along the lines of this guiding theme, we will stimulate scientific discussions about all aspects in basic and applied ecological research contributing to better connect.

Policy-makers and science and industry representatives are discussing how to make large amounts of Earth observation data accessible to a wider user community. To explore this idea, some 250 science, industry and policy-making representatives and national delegates from Europe, the US, Australia, China and Africa met at ESA’s ESRIN centre in Frascati, Italy last week for ESA’s first ‘Big Data from Space’ event.

Representatives from ESA and NASA opened the event together with the European Commission. European Commission Directorates-General for Enterprise and Industry, Research and Innovation and Communications Networks, Content and Technology, along with representatives from the European Environment Agency, the National Oceanic and Atmospheric Administration and the Open Geospatial Consortium acted as session chairs. 

Javier de la Torre, representing the EU BON partner Vizzuality gave a presentation 'Global Deforestation through Timeme: Big Data Meets Scalable Visualizations,' which included some of the work Vizzuality is doing toward the EUBON project.

The event concluded with a strong call by all parties for the ability to handle and use big Earth observing data. This could potentially open new opportunities for research and international cooperation schemes such as programmatic and industrial coordination.