2
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      The Open Biodiversity Knowledge Management (eco-)System: Tools and Services for Extraction, Mobilization, Handling and Re-use of Data from the Published Literature

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The Open Biodiversity Knowledge Management System (OBKMS) is an end-to-end, eXtensible Markup Language (XML)- and Linked Open Data (LOD)-based ecosystem of tools and services that encompasses the entire process of authoring, submission, review, publication, dissemination, and archiving of biodiversity literature, as well as the text mining of published biodiversity literature (Fig. 1). These capabilities lead to the creation of interoperable, computable, and reusable biodiversity data with provenance linking facts to publications. OBKMS is the result of a joint endeavour by Plazi and Pensoft lasting many years. The system was developed with the support of several biodiversity informatics projects - initially (Virtual Biodiversity Research and Access Network for Taxonomy) ViBRANT, and then followed by pro-iBiosphere, European Biodiversity Observation Network (EU BON), and Biosystematics, informatics and genomics of the big 4 insect groups (BIG4). The system includes the following key components: ARPHA Journal Publishing Platform: a journal publishing platform based on the TaxPub XML extension for National Library of Medicine (NLM)’s Journal Publishing Document Type Definition (DTD) (Version 3.0). Its advanced ARPHA-BioDiv component deals with integrated biodiversity data and narrative publishing (Penev et al. 2017). GoldenGATE Imagine: an environment for marking up, enhancing, and extracting text and data from PDF files, supporting the TaxonX XML schema. It has specific enhancements for articles containing descriptions of taxa ("taxonomic treatments") in the field of biological systematics, but its core features may be used for general purposes as well. Biodiversity Literature repository (BLR): a public repository hosted at Zenodo (CERN) for published articles (PDF and XML) and images extracted from articles. Ocellus/Zenodeo: a search interface for the images stored at BLR. TreatmentBank: an XML-based repository for taxonomic treatments and data therein extracted from literature. The OpenBiodiv knowledge graph: a biodiversity knowledge graph built according to the Linked Open Data (LOD) principles. Uses the RDF data model, the SPARQL Protocol and RDF Query Language (SPARQL) query language, is open to the public, and is powered by the OpenBiodiv-O ontology (Senderov et al. 2018). OpenBiodiv portal: Semantic search and browser for the biodiversity knowledge graph. Multiple semantic apps packaging specific views of the biodiviersity knowledge graph. Supporting tools: Pensoft Markup Tool (PMT) ARPHA Writing Tool (AWT) ReFindit R libraries for working with RDF and for converting XML to RDF (ropenbio, RDF4R). Plazi RDF converter, web services and APIs. As part of OBKMS, Plazi and Pensoft offer the following services beyond supplying the software toolkit: Digitization through imaging and text capture of paper-based or digitally born (PDF) legacy literature. XML markup of both legacy and newly published literature (journals and books). Data extraction and markup of taxonomic names, literature references, taxonomic treatments and organism occurrence records. Export and storage of text, images, and structured data in data repositories. Linking and semantic enhancement of text and data, bibliographic references, taxonomic treatments, illustrations, organism occurrences and organism traits. Re-packaging of extracted information into new, user-demanded outputs via semantic apps at the OpenBiodiv portal. Re-publishing of legacy literature (e.g., Flora, Fauna, and Mycota series, important biodiversity monographs, etc.). Semantic open access publishing (including data publishing) of journal and books. Integration of biodiversity information from legacy and newly published literature into interoperable biodiversity repositories and platforms (Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL), Species-ID, Plazi, Wikidata, and others). In this presentation we make the case for why OpenBiodiv is an essential tool for advancing biodiversity science. Our argument is that through OpenBiodiv, biodiversity science makes a step towards the ideals of open science (Senderov and Penev 2016). Furthermore, by linking data from various silos, OpenBiodiv allows for the discovery of hidden facts. A particular example of how OpenBiodiv can advance biodiversity science is demonstrated by the OpenBiodiv's solution to "taxonomic anarchy" (Garnett and Christidis 2017). "Taxonomic anarchy" is a term coined by Garnett and Christidis to denote the instability of taxonomic names as symbols for taxonomic meaning. They propose an "authoritarian" top-down approach to stablize the naming of species. OpenBiodiv, on the other hand, relies on taxonomic concepts as integrative units and therefore integration can occur through alignment of taxonomic concepts via Region Connection Calculus (RCC-5) (Franz and Peet 2009). The alignment is "democratically" created by the users of system but no consensus is forced and "anarchy" is avoided by using unambiguous taxonomic concept labels (Franz et al. 2016) in addition to Linnean names.

          Related collections

          Most cited references 5

          • Record: found
          • Abstract: not found
          • Article: not found

          Perspectives: Towards a language for mapping relationships among taxonomic concepts

           N.M. Franz,  R.K. Peet (2009)
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system

            Background The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy. Results OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses. Conclusions OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System. Electronic supplementary material The online version of this article (doi:10.1186/s13326-017-0174-5) contains supplementary material, which is available to authorized users.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found
              Is Open Access

              The Open Biodiversity Knowledge Management System in Scholarly Publishing

              This project aims to develop and implement novel ways of publication, visualization, and dissemination of biodiversity and biodiversity-related data and thus bring the Open Biodiversity Knowledge Management System closer to fruition. In order to do so, we will develop new types of Enhanced Publications (EP's), which will allow automated data import into the manuscript and export from the manuscript and provide dynamic visualizations. These EP's will enable biodiversity researchers and taxonomists to streamline their work and publish more data-rich species descriptions.
                Bookmark

                Author and article information

                Journal
                Biodiversity Information Science and Standards
                BISS
                Pensoft Publishers
                2535-0897
                May 17 2018
                May 17 2018
                : 2
                Article
                10.3897/biss.2.25748
                © 2018

                Comments

                Comment on this article