The EU BON project is pleased to announce the International Symposium "Nature and Governance – Biodiversity Data, Science, and the Policy Interface", which was held in Berlin from 11 to 12 February. The symposium aimed at clarifying and popularizing EU BON's objectives prior to the official EU BON Kick-off Meeting held from 13 to 15 February 2013.

The symposium was hosted by the Museum für Naturkunde Berlin and brought together high-ranking speakers and guests from across the world to talk and discuss the different aspects of the EU BON Project. Among the main issues covered was the future of biodiversity information, the challenges in front of new data policies, new approaches in collecting information, and ways to engage the public in biodiversity monitoring and assessments.

The EU BON project was started on 1 December, 2012, and will continue for 4.5 years. The aim of EU BON is to build a substantial part and contribute to the Group on Earth Observation's Biodiversity Observation Network (GEO BON), through an innovative approach of integration of biodiversity information systems. The project, built as an answer to the need of a new integrated biodiversity data, will facilitate access to this knowledge and will effectively improve the work in the field of biodiversity observation in general.

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For more information on the symposium and the events planned, please visit our programme page.

All interested parties are most welcome to attend the symposium or to follow it on Twitter, Facebook, or Google+.

Additional information

EU BON (2012) stands for "Building the European Biodiversity Observation Network" and is a European research project, financed by the 7th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

GEO BON stands for "Group on Earth Observations Biodiversity Observation Network". It coordinates activities relating to the Societal Benefit Area (SBA) on Biodiversity of the Global Earth Observation System of Systems (GEOSS). Some 100 governmental, inter-governmental and non-governmental organisations are collaborating through GEO BON to organise and improve terrestrial, freshwater and marine biodiversity observations globally and make their biodiversity data, information and forecasts more readily accessible to policymakers, managers, experts and other users. Moreover, GEO BON has been recognized by the Parties to the Convention on Biological Diversity. More information at: http://www.earthobservations.org/geobon.shtml.

Zur Unterstützung der Beteiligung des MfN an EU BON ist am Museum für Naturkunde Berlin zum nächstmöglichen Zeitpunkt eine vorerst auf 2 Jahre befristete (mit der Option der Verlängerung)
Position eines/einer Wissenschaftlichen Mitarbeiters/in mit 75% der regelmäßigen wöchentlichen Arbeitszeit Entgeltgruppe E13 TV-L Berlin zu besetzen
Aufgabengebiete:
Wissenschaftliche Mitarbeit und eigenständige Durchführung spezifischer Aufgaben innerhalb des EU BON Projektes, vor allem innerhalb der Arbeitspakete 1 (Datenquellen) und 2 (Datenintegration), i.b.
- Datenrecherche und Erstellung von Übersichten für EU BON relevanter Daten- und Informationsquellen;
- Bewertung und Lückenanalyse bestehender Datenbanken und Informationssysteme zur Biodiversität;
- Harmonisierung, Aktualisierung und Koordinierung taxonomischer Referenz-Datenbanken i.b. für Europa;
- Unterstützung der Einführung und Verbesserung von Datenstandards zur Verbesserung der Integration und Interoperabilität unterschiedlicher Datenebenen
- Mitwirkung bei Erprobung neuer Datenerhebungsansätze und –verfahren, auch im Gelände
- Planung und Durchführung von Projekttreffen und -veranstaltungen
- Erstellung von Ergebnisberichten und wissenschaftlichen Präsentationen / Veröffentlichungen.

Huge data encompassed into a unique georeferenced macrobenthic assemblages database

A new peer-reviewed data paper offers a comprehensive, open-access collection of georeferenced biological information about the Antarctic macrobenthic communities. The term macrobenthic refers to the visible-for-the-eye organisms that live near or on the sea bottom such as echinoderms, sponges, ascidians, crustaceans. The paper will help in coordinating biodiversity research and conservation activities on species living near the ocean bottom of the Antarctic.
The data paper "Antarctic macrobenthic communities: A compilation of circumpolar information", published in the open access journal Nature Conservation, describes data from approximately 90 different expeditions in the region since 1956 that have now been made openly available under a CC-By license. The paper provides unique georeferenced biological basic information for the planning of future coordinated research activities, for example those under the umbrella of the biology program Antarctic Thresholds – Ecosystem Resilience and Adaptation (AnT-ERA) of the Scientific Committee on Antarctic Research (SCAR). The information collected could be also beneficial for current conservation priorities such as the planning of Marine Protected Areas (MPAs) by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).
The expeditions were organised by several famous explorers of the Antarctic. The area covered by the paper consists of almost the entire Southern Ocean, including sites covered by a single ice-shelf. The vast majority of information is from shelf areas around the continent at water depth shallower than 800m. The information from the different sources is then attributed to the classified macrobenthic assemblages. The results are made publicly available via the "Antarctic Biodiversity Facility" (data.biodiversity.aq).
A specific feature of this paper is that the manuscript was automatically generated from the Integrated Publishing Toolkit of the Antarctic Node of the Global Biodiversity Information Facility (AntaBIF IPT) and then submitted to the journal Nature Conservation through a novel workflow developed by GBIF and Pensoft Publishers. (see previous press release). Data are made freely available through the AntaBIF IPT, and sea-bed images of 214 localities through the data repository for geoscience and environmental data, PANGAEA- Data Publisher for Earth and Environmental Science (sample: http://doi.pangaea.de/10.1594/PANGAEA.198682).

A new "LinkOut" feature introduced by the National Center for Biotechnology Information (NCBI) NCBI’s allows the easy linking to content on PubMed and GenBank.  Dryad has already introduced the feature benefitting from easy and fast linking of associated content to the two resources.

PubMed and GenBank, from the National Center for Biotechnology Information (NCBI), are hugely popular resources for searching and retrieving article abstracts and nucleotide sequence data, respectively.  PubMed indexes the vast majority of the biomedical literature, and deposition of nucleotide sequences in GenBank or one of the other INSDC databases is a near universal requirement for publication in a scientific journal. LinkOut allows the data from an article to be distributed among repositories without compromising its discoverability.

Dryad, intends to expand on this feature in a couple of ways. First, it is planned to make Dryad content searchable via the PubMed and GenBank identifiers, which because of their wide use will provide a convenient gateway for other biomedical databases to link out to Dryad.  Second, open web standards will be used to expose relationships between content in Dryad and other repositories, not just NCBI.

Original source: Dryad news and views

The Research Data Alliance (RDA) has been recently launched. Its First Plenary took place between 18-20 March, 2013 in Gothenburg, Sweden. The hot topic of the Plenary was the RDA vision towards open access data without barriers. The 3 days of meetings and working sessions brought the research data community together to contribute and set milestones for the future work of the RDA towards open access data-driven innovation. 

Over the last decade, significant investments have been made  all over the globe
for developing scientific  data infrastructures to support the work of research communities and improving shared access to data.  There is a  common understanding that solutions must be global and that the development of an integrated and interoperable data domain can only be achieved through increased global cooperation.

As "big data" emerges as an international priority, the Research Data Alliance (RDA) is a newly formed organization whose goal is to accelerate data-driven innovation world-wide through research data sharing and exchange.

At its first Plenary, the RDA was launched by sponsors from the European Commission, the U. S. Government and the Australian Government and leaders in the data community. The Plenary was used as a working meeting to accelerate discussion, Working and Interest Group interaction, and data community development.

ICSU-WDS Data Publication Charter: http://www.icsu-wds.org/working-groups/data-publication

One year of experience and perspectives for the future from Pensoft Publishers and GBIF

In 2012 GBIF and Pensoft pioneered a workflow between the GBIF’s Integrated Publishing Toolkit (IPT) and Pensoft’s journals ZooKeys, PhytoKeys, MycoKeys, Nature Conservation, etc. to automatically export metadata into the form of a data paper manuscript, based on the Ecological Metadata Language (EML). One year on they share their experience and perspectives for the future of data publishing.

In its essence, a Data Paper is a scholarly journal publication whose primary purpose is to describe a dataset or a group of datasets, rather than to report a research investigation. As such, it contains facts about data, not hypotheses and arguments in support of the data, as found in a conventional research article. The future of data publishing according to Pensoft Publishers and GBIF, lies in the elaborating of formats for descriptions of various kinds of data (ecological, morphological, genomic, environmental, etc.), as well as in linking to various platforms (GBIF, Scratchpads, Dryad, EDIT, CBOL, etc.).

More about the collaboration and experience of Pensoft Publishers and GBIF learn from their joint poster available here.

The first meeting of Work Package 5 (EU BON testing and validation of concepts, tools, and services) was held between 2^nd and 4^th April, 2013 in the Doñana Biological Station, in Spain. 23 people from 10 different institutions (7 of the EU BON consortium) worked towards building a draft on Principles and Guidelines for establishing and operating EU BON test sites.

During the meeting the members agreed on starting documenting each of the sites, using a common format to be decided in May on the Informatics Task Force meeting of WP2 (Data integration and interoperability) in Norway. A data inventory will also be built in each of the sites, adding monitoring protocols in stepwise fashion.

In addition the meeting served to get a better view of the variety of Ecosystems in Doñana as well as the monitoring protocols that are being conducted in this area. 

A new article "A decadal view of biodiversity informatics: challenges and priorities"  published by BMC Ecology focuses on the challenges and perspectives for biodiversity informatics after a decade of development. The authors Alex Hardisty and Dave Roberts alongside 77 contributions from the biodiversity informatics community share experience and set future directions of biodiversity informatics as a tool for addressing conservation and ecological issues.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

The full text of the article can be accessed here.

November 19-22, 2013 Alexander Technological Educational Institute of Thessaloniki, Greece

Continuing the successful mission of previous MTSR Conferences (MTSR'05, MTSR'07, MTSR'09, MTSR'10, MTSR'11 and MTSR’12), the seventh International Conference on Metadata and Semantics Research (MTSR'13) aims to bring together scholars and practitioners that share a common interest in the interdisciplinary field of metadata, linked data and ontologies. Participants will share novel knowledge and best practice in the implementation of these semantic technologies across diverse types of Information Environments and applications. These include Cultural Informatics; Open Access Repositories & Digital Libraries; E-learning applications; Search Engine Optimisation & Information Retrieval; Research Information Systems and Infrastructures; e-Science and e-Social Science applications; Agriculture, Food and Environment; Bio-Health & Medical Information Systems.

Science for Environment Policy features a policy brief explaining the biases around biodiversity databases in their latest issue 331, from 6 June 2013. "Biodiversity databases: language and location help explain biases" features a new study arguing that low numbers of English speakers, large distances from the database host and low security acting as key barriers to data collection and among the main reasons for the underrepresentation of some countries in biodiversity databases.

Source: Amano T., Sutherland W.J. (2013) Four barriers to the global understanding of biodiversity conservation: wealth, language, geographical location and security. Proceedings of the Royal Society B. 280: 20122649. doi: 10.1098/rspb.2012.2649

The Brazilian initiative PPBio (The Program for Research on Biodiversity) launches a new book based on over a decade of experience in implementing the biodiversity monitoring system RAPELD in the Brazilian Amazon. Richly illustrated and written in simple language, the book "Biodiversity and Integrated Environmental Monitoring" addresses the issues that led to the system development, covering topics such as the spatial organization and representation of biological diversity, environmental monitoring, and data management.

Monitoring of biodiversity is not merely an academic endeavor. Although scientific aspects such as representation of biodiversity and biodiversity data integration, management and preservation are of a great importance, it is also essential to think about the political context in which decisions will be made and how to incorporate political stakeholders and decision makers.

"As this important book makes clear questions about biodiversity are far from purely scientific. Biodiversity matters. Our needs to assess it embed in a complex of questions posed by managers, policy makers and those who live in or otherwise benefit from biodiversity.",  explains Dr Stuart L. Pimm in the preface of the book. "So how do we ensure that data collected now will be useful for purposes we cannot yet imagine at some unexpected time in the future? Or provide comparison to some other place that we might survey some day?"

Those and many more questions regarding biodiversity data management and policy involvement are discussed in the new book "Biodiversity and Integrated Environmental Monitoring".

The University of Cambridge invites for applications for a Research Associate to work on EU-BON, a major EU-funded research project seeking to improve the use of biodiversity data in public policy.

Applicants should have a PhD in a relevant social science or conservation science. Experience in both qualitative and quantitative analysis is desirable. Applicants should ideally have some first-hand experience of public policy processes and a willingness to travel within the European Union for research. Excellent organisational and communication skills will be essential in working as a successful part of this large, multi-partner and multinational team.

The researcher will carry out research on how biodiversity data is currently used in European policy making and will contribute to analysis of the opportunities to increase its effective provision and use. Research methods are likely to combine qualitative and quantitate analysis and to focus on the use of biodiversity data in public policy contexts. It is expected that some of the research will take place in Brussels. The researcher will have considerable freedom in defining the research project in discussion with Dr Doubleday and Prof Sutherland. In addition to carrying out research on the use of biodiversity data in European policy making, the researcher will support Cambridge's contribution to EU BON as a whole. This will involve contributing to other workpackages as and when required. More information about EU BON can be found here: http://www.eubon.eu

Fixed-term: The funds for this post are available for 36 months in the first instance.

Completed applications consisting of a CHRIS/6 (Parts I & III) (downloadable from http://www.admin.cam.ac.uk/offices/hr/forms/chris6/) a covering letter, and CV, should be sent to Danielle Feger, via email: geogrec@hermes.cam.ac.uk or sent to Research Administrator, Department of Geography, Downing Site, Cambridge, CB2 3EN

Please quote reference LC01355 on your application and in any correspondence about this vacancy.

Any enquiries concerning the position can be made to Dr Robert Doubleday, rob.doubleday@csap.cam.ac.uk

For more information about the position, please visit: http://www.jobs.cam.ac.uk/job/1611/

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.

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

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

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

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 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.

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 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.

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."

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.

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)

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)

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"

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

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

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

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

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

SeaLifeBase: www.sealifebase.ca

Four papers on species traits have been recently published in ZooKeys, Ecology and Ecology, Evolution and the Biodiversity Data Journal respectivelly covering data on the butterflies in Europe, birds and mammals of the world, the terrestrial mammals of the world and marine polychaetes.

Schweiger O, Harpke A, Wiemers M, Settele J (2014) CLIMBER: Climatic niche characteristics of the butterflies in Europe. ZooKeys 367: 65–84. doi: 10.3897/zookeys.367.6185 Resource ID: GBIF key: http://www.gbif.org/dataset/e2bcea8c-dfea-475e-a4ae-af282b4ea1c5

Hamish Wilman, Jonathan Belmaker, Jennifer Simpson, Carolina de la Rosa, Marcelo M. Rivadeneira, and Walter Jetz. 2014. EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals. Ecology 95:2027. http://dx.doi.org/10.1890/13-1917.1

Kissling, W. D., Dalby, L., Fløjgaard, C., Lenoir, J., Sandel, B., Sandom, C., Trøjelsgaard, K. and Svenning, J.-C. (2014), Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide. Ecology and Evolution. doi: 10.1002/ece3.1136

Faulwetter S, Markantonatou V, Pavloudi C, Papageorgiou N, Keklikoglou K, Chatzinikolaou E, Pafilis E, Chatzigeorgiou G, Vasileiadou K, Dailianis T, Fanini L, Koulouri P, Arvanitidis C (2014) Polytraits: A database on biological traits of marine polychaetes. Biodiversity Data Journal 2: e1024. DOI: 10.3897/BDJ.2.e1024

The August 2014 updates of FishBase are now available online!
See: www.fishbase.us, www.fishbase.ca, www.fishbase.sa 

FishBase stats to date: (32900 Species, 303000 Common names, 54800 Pictures, 51400 References, 2150 Collaborators, 800000 Visits/Month)

Thanks for your continuous patronage and support!

Fauna Europaea started in 2000 as an EC-FP5 four-year project, delivering its first release in 2004. After 14 years of steady progress and successful participations in several EC projects, as a part of the EC-FP7 European Biodiversity Observation Network project (EU BON), to increase the general awareness of the work done by the contributors and to extend the general dissemination of the Fauna Europaea results, the Biodiversity Data Journal has applied its novel e-Publishing tools to prepare data papers for all 56 major taxonomic groups.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level, and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 species name. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education.

'Contributions on Fauna Europaea' is the second series launched by the Biodiversity Data Journal after the Checklist of British and Irish Hymenoptera and the first one that embraces thematic data-papers structured in a common pattern extracted from a large database. This novel publication model will assemble in a single-issue 56 data-papers on different taxonomic groups covered by the Fauna Europaea project in the period 2000-2014 and a range of accompanying papers highlighting various aspects of this project (gap-analysis, software design, taxonomic assessments, etc.).

This is the first collection of data-papers of this scale. It will formalise and effectively publish the results of nearly 500 contributors building the largest European animal (taxonomic) database. The new publication model provides a reliable mechanism for citation and bibliographic indexing of large and uniformly structured databases.

"The publication of Fauna Europaea data papers brings a number of benefits for science, for example it stimulates experts to hand-over descriptive details on their groups, triggers new ways of community networking and participation, motivates experts to update their data, supports a better documentation of their achievements, including issues like 'micro-publications', and increase an ownership feeling with the associated effort" said Dr Yde de Jong, coordinator of the Fauna Europaea and Pan-European Species directories Infrastructure (PESI) projects.

The launch of this large collection of data papers coincides with one more cutting-edge innovation of the Biodiversity Data Journal, the publication of an API, a first of its kind, to import complex and data-rich manuscripts, which include text, data, images, in-text citations, references, in fact anything that a manuscript may contain.

"I am happy that these exciting innovations coincided with the first birthday of the Biodiversity Data Journal. Just a year ago we launched this new concept with the motto: Making your data count! These novel approaches and tools are an excellent example how our concept evolved!" comments Prof. Lyubomir Penev, Managing Director of Pensoft Publishers.

Original Sources:

de Jong Y, Verbeek M, Michelsen V, Bjørn P, Los W, Steeman F, Bailly N, Basire C, Chylarecki P, Stloukal E, Hagedorn G, Wetzel F, Glöckler F, Kroupa A, Korb G, Hoffmann A, Häuser C, Kohlbecker A, Müller A, Güntsch A, Stoev P, Penev L (2014) Fauna Europaea – all European animal species on the web. Biodiversity Data Journal 2: e4034. doi: 10.3897/BDJ.2.e4034

Gibson D, Bray R, Hunt D, Georgiev B, Scholz T, Harris P, Bakke T, Pojmanska T, Niewiadomska K, Kostadinova A, Tkach V, Bain O, Durette-Desset M, Gibbons L, Moravec F, Petter A, Dimitrova Z, Buchmann K, Valtonen E, de Jong Y (2014) Fauna Europaea: Helminths (Animal Parasitic). Biodiversity Data Journal 2: e1060. doi: 10.3897/BDJ.2.e1060

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

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

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

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

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

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

Original Source:

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

Additional information:

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

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

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

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

Data sharing tools developed by an EU project are helping scientists worldwide understand more about the planet’s millions of species. A new article published on CORDIS and DAE looks into the benefits of the FP7 funded project VIBRANT.

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

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

The consultation will run from the 7th of October to the 30th of November 2014. Comments received before the 31st of October 2014 will be, as much as possible, presented with the first results of this project during the IUCN World Parks Congress taking place in Sydney, Australia, 12-19 November 2014.

Contributors are not required to comment on the entire Consultation Document – any input will welcomed. 

More information available here.

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

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

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

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

The DE domain is recently acquired.

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

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

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

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

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

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

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

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

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

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

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Original Source:

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

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

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

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

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

The 40 attendees came from 18 different countries.

Participants at the meeting.

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

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

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

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

Results of the recently published study show:

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

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

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

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

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

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Original Source:

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

Additional information:

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