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

Author

Listed:
  • Lyubomir Penev

    (Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
    Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria)

  • Mariya Dimitrova

    (Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
    Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 25A, 1113 Sofia, Bulgaria)

  • Viktor Senderov

    (Swedish Museum of Natural History, Frescativägen 40, 114 18 Stockholm, Sweden)

  • Georgi Zhelezov

    (Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria)

  • Teodor Georgiev

    (Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria)

  • Pavel Stoev

    (Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
    National Museum of Natural History, 1 Tsar Osvoboditel Blvd, 1000 Sofia, Bulgaria)

  • Kiril Simov

    (Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 25A, 1113 Sofia, Bulgaria)

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.

Suggested Citation

  • Lyubomir Penev & Mariya Dimitrova & Viktor Senderov & Georgi Zhelezov & Teodor Georgiev & Pavel Stoev & Kiril Simov, 2019. "OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science," Publications, MDPI, vol. 7(2), pages 1-16, May.
    • Handle: RePEc:gam:jpubli:v:7:y:2019:i:2:p:38-:d:235319
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    Cited by:

    1. Stefano Ferilli & Eleonora Bernasconi & Davide Di Pierro & Domenico Redavid, 2023. "A Graph DB-Based Solution for Semantic Technologies in the Future Internet," Future Internet, MDPI, vol. 15(10), pages 1-28, October.

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