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Open AccessArticle

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

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Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
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Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
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Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 25A, 1113 Sofia, Bulgaria
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Swedish Museum of Natural History, Frescativägen 40, 114 18 Stockholm, Sweden
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National Museum of Natural History, 1 Tsar Osvoboditel Blvd, 1000 Sofia, Bulgaria
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Author to whom correspondence should be addressed.
Publications 2019, 7(2), 38; https://doi.org/10.3390/publications7020038
Received: 23 April 2019 / Revised: 21 May 2019 / Accepted: 24 May 2019 / Published: 29 May 2019
(This article belongs to the Special Issue New Frontiers for Openness in Scholarly Publishing)
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. View Full-Text
Keywords: open science; biodiversity; biodiversity informatics; knowledge management system; semantic publishing; Linked Open Data; Semantic Web; ontology open science; biodiversity; biodiversity informatics; knowledge management system; semantic publishing; Linked Open Data; Semantic Web; ontology
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Penev, L.; Dimitrova, M.; Senderov, V.; Zhelezov, G.; Georgiev, T.; Stoev, P.; Simov, K. OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science. Publications 2019, 7, 38.

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