OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science

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Abstract

Hundreds of years of biodiversity research have resulted in the accumulation of a substantial pool of communal knowledge; however, most of it is stored in silos isolated from each other, such as published articles or monographs. The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management System (OBKMS). This paper presents OpenBiodiv: An OBKMS that utilizes semantic publishing workflows, text and data mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for managing biodiversity knowledge. It is presented as a Linked Open Dataset generated from scientific literature. OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Through the application of semantic technologies, the project showcases the value of open publishing of Findable, Accessible, Interoperable, Reusable (FAIR) data towards the establishment of open science practices in the biodiversity domain.

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Denny Vrandečić, Markus Krötzsch (2014)

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Names are key to the big new biology.

Arthur J L Cooper, David Remsen, Scott D. Patterson … (2010)

Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture. Copyright © 2010 Elsevier Ltd. All rights reserved.

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Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples

Lyubomir Penev, Donat Agosti, Teodor Georgiev … (2010)

Abstract The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.