Biodiversity data import from historical literature assessed in an EMODnet Workshop Report

While biodiversity loss is an undisputable issue concerning everyone on a global scale, data about species distribution and numbers through the centuries is crucial for adopting adequate and timely measures.

However, as abundant as this information currently is, large parts of the actual data are locked-up as scanned documents, or not digitized at all. Far from the machine-readable knowledge, this information is left effectively inaccessible. In particular, this is the case for data from marine systems.

This is how data managers who implement data archaeology and rescue activities, as well as external experts in data mobilization and data publication, were all brought together in Crete for the European Marine Observation and Data network (EMODnet) Workshop, which is now reported in the open access journal Research Ideas and Outcomes (RIO).

“In a time of global change and biodiversity loss, information on species occurrences over time is crucial for the calculation of ecological models and future predictions”, explain the authors. “But while data coverage is sufficient for many terrestrial areas and areas with high scientific activity, large gaps exist for other regions, especially concerning the marine systems.”

Aiming to fill both spatial and temporal gaps in European marine species occurrence data availability by implementing data archaeology and rescue activities, the workshop took place on 8th and 9th June in 2015 at the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, Greece. There, the participants joined forces to assess possible mechanisms and guidelines to mobilize legacy biodiversity data.

Together, the attendees reviewed the current issues associated with manual extraction of occurrence data. They also used the occasion to test tools and mechanisms that could potentially support a semi-automated process of data extraction. Long-disputed in the scholarly communities matters surrounding data re-publication, such as openly accessible data and author attribution were also discussed. As a result, at the end of the event, a list of recommendations and conclusions was compiled, also openly available in the Workshop Report publication.

Ahead of the workshop, curators extracted legacy data to compile a list of old faunistic reports, based on certain criteria. While performing the task, they noted the time and the problems they encountered along the way. Thus, they set the starting point for the workshop, where participants would get the chance to practice data extraction themselves at the organised hands-on sessions.

“Legacy biodiversity literature contains a tremendous amount of data that are of high value for many contemporary research directions. This has been recognized by projects and institutions such as the Biodiversity Heritage Library (BHL), which have initiated mass digitization of century-old books, journals and other publications and are making them available in a digital format over the internet,” note the authors.

“However, the information remains locked up even in these scanned files, as they are available only as free text, not in a structured, machine-readable format”.

In conclusion, the participants at the European Marine Observation and Data network¬†Workshop listed practical tips regarding in-house document scanning; suggested a reward scheme for data curators, pointing out that credit needs to be given to the people “who made these valuable data accessible again”; encouraged Data papers publication, for aligning with the “emerging success of open data”; and proposed the establishment of a data encoding schema. They also highlighted the need for academic institutions to increase their number of professional data manager permanent positions, while also providing quality training to long-term data experts.

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Original source:

Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. doi: 10.3897/rio.2.e9774

Sharing biodiversity data: Best tools and practices via the EU-funded project EU BON

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

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

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

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

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

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

Envisaged information flows between EU BON and LTER Europe, showing the complexity of sharing biodiversity data (from the 3rd EU BON Stakeholder Roundtable, Granada on 9-11 December 2015).
Envisaged information flows between EU BON and LTER Europe, showing the complexity of sharing biodiversity data (from the 3rd EU BON Stakeholder Roundtable, Granada on 9-11 December 2015).

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

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Original Source:

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

 

About EU BON:

EU BON 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.