Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

The OpenBiodiv contribution to BiCIKL

Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.

In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.

“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”

explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.

“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”

he adds.

At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.

Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL. 

As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions. 

Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.

Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.

On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.

Sample of predefined SPARQL queries at OpenBiodiv.

“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”

concludes Prof Lyubomir Penev.

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Follow BiCIKL on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

You can also follow Pensoft on Twitter, Facebook and Linkedin and use #OpenBiodiv on Twitter.

LifeWatchGreece launches a Special Paper Collection for Greek biodiversity research

Developed in the 1990s and early 2000s, LifeWatch is one of the large-scale European Research Infrastructures (ESFRI) created to support biodiversity science and its developments. Its ultimate goal is to model Earth’s biodiversity based on large-scale data, to build a vast network of partners, and to liaise with other high-quality and viable research infrastructures (RI).

Being one of the founding LifeWatch member states, Greece has not only implemented LifeWatchGreece, but it is all set and ready to “fulfill the vision of the Greek LifeWatch RI and establish it as the biodiversity Centre of Excellence for South-eastern Europe”, according to the authors of the latest Biodiversity Data Journal‘s Editorial: Dr Christos Arvanitidis, Dr Eva Chatzinikolaou, Dr Vasilis Gerovasileiou, Emmanouela Panteri, Dr Nicolas Bailly, all affiliated with the Hellenic Centre for Marine Research (HCMR) and part of the LifeWatchGreece Core Team, together with Nikos Minadakis, Foundation for Research and Technology Hellas (FORTH), Alex Hardisty, Cardiff University, and Dr Wouter Los, University of Amsterdam.

lwg-presentationMaking use of the technologically advanced open access Biodiversity Data Journal and its Collections feature, the LifeWatchGreece team is publishing a vast collection of peer-reviewed scientific outputs, including software descriptions, data papers, taxonomic checklists and research articles, along with the accompanying datasets and supporting material. Their intention is to demonstrate the availability and applicability of the developed e-Services and Virtual Laboratories (vLabs) to both the scientific community, as well as the broader domain of biodiversity management.

The LifeWatchGreece Special Collection is now available in Biodiversity Data Journal, with a series of articles highlighting key contributions to the large-scale European LifeWatch RI. The Software Description papers explain the LifeWatchGreece Portal, where all the e-Services and the vLabs provided by LifeWatchGreece RI are hosted; the Data Services based on semantic web technologies, which provide detailed and specialized search paths to facilitate data mining; the R vLab which can be used for a series of statistical analyses in ecology, based on an integrated and optimized online R environment; and the Micro-CT vLab, which allows the online exploration, dissemination and interactive manipulation of micro-tomography datasets.

The LifeWatchGreece Special Collection also includes a series of taxonomic checklists (preliminary, updated and/or annotated); a series of data papers presenting historical and original datasets; and a selection of research articles reporting on the outcomes, methodologies and citizen science initiatives developed by collaborating research projects, which have shared human, hardware and software resources with LifeWatchGreece RI.

LifeWatchGreece relies on a multidisciplinary approach, involving several subsidiary initiatives; collaborations with Greek, European and World scientific communities; specialised staff, responsible for continuous updates and developments; and, of course, innovative online tools and already established IT infrastructure.

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Original source:

Arvanitidis C, Chatzinikolaou E, Gerovasileiou V, Panteri E, Bailly N, Minadakis N, Hardisty A, Los W (2016) LifeWatchGreece: Construction and operation of the National Research Infrastructure (ESFRI). Biodiversity Data Journal 4: e10791. https://doi.org/10.3897/BDJ.4.e10791

Additional information:

This work has been supported by the LifeWatchGreece infrastructure (MIS 384676), funded by the Greek Government under the General Secretariat of Research and Technology (GSRT), ESFRI Projects, National Strategic Reference Framework (NSRF).