SpringerLink
Log in

BiodivOnto: Towards a Core Ontology for Biodiversity

  • Conference paper
  • First Online:
The Semantic Web: ESWC 2021 Satellite Events (ESWC 2021)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 12739))

Included in the following conference series:

Abstract

Biodiversity is the variety of life on earth which covers the evolutionary, ecological, and cultural processes that sustain life. Therefore, it is important to understand where biodiversity is, how it is changing over space and time, the driving factors of these changes and the resulting consequences on the diversity of life. To do so, it is necessary to describe and integrate the conditions and measures of biodiversity to fully capture the domain. In this paper, we present the design of a core ontology for biodiversity aiming to establish a link between the foundational and domain-specific ontologies. The proposed ontology is designed using the fusion/merge strategy by reusing existing ontologies and it is guided by data from several resources in the biodiversity domain.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

Notes

  1. 1.

    https://ipbes.net/global-assessment.

  2. 2.

    https://bioportal.bioontology.org/ontologies/ENVO.

  3. 3.

    https://bioportal.bioontology.org/ontologies/IOBC.

  4. 4.

    https://bioportal.bioontology.org/ontologies/BFO.

  5. 5.

    https://bioportal.bioontology.org/ontologies/GFO.

  6. 6.

    https://bioportal.bioontology.org/.

  7. 7.

    http://agroportal.lirmm.fr.

  8. 8.

    https://china.befdata.biow.uni-leipzig.de/.

  9. 9.

    https://data.world/.

  10. 10.

    https://github.com/fusion-jena/BiodivOnto/tree/main/data.

  11. 11.

    https://bioportal.bioontology.org/ontologies/SWEET.

  12. 12.

    https://bioportal.bioontology.org/ontologies/ECOCORE.

  13. 13.

    https://bioportal.bioontology.org/ontologies/ECSO.

  14. 14.

    https://bioportal.bioontology.org/ontologies/CBO.

  15. 15.

    https://bioportal.bioontology.org/ontologies/BCO.

  16. 16.

    https://www.biodiversitya-z.org/.

  17. 17.

    http://www.aquadiva.uni-jena.de/.

  18. 18.

    https://bioportal.bioontology.org/ontologies/PATO.

  19. 19.

    https://github.com/fusion-jena/BiodivOnto.

References

  1. Faessler, E., Hahn, U.: Semedico: a comprehensive semantic search engine for the life sciences. In: Proceedings of ACL 2017, System Demonstrations, July 2017

    Google Scholar 

  2. Faessler, E., Klan, F., Algergawy, A., König-Ries, B., Hahn, U.: Selecting and tailoring ontologies with JOYCE. In: Ciancarini, P., et al. (eds.) EKAW 2016. LNCS (LNAI), vol. 10180, pp. 114–118. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-58694-6_12

    Chapter  Google Scholar 

  3. Fathalla, S., Vahdati, S., Auer, S., Lange, C.: SemSur: a core ontology for the semantic representation of research findings. In: SEMANTICS (2018)

    Google Scholar 

  4. Garcia, L.F., et al.: The GeoCore ontology: a core ontology for general use in geology. Comput. Geosci. 135, 104387 (2020)

    Article  Google Scholar 

  5. Goldberg, Y., Levy, O.: word2vec explained: deriving Mikolov et al’.s negative-sampling word-embedding method. ar**v preprint ar**v:1402.3722 (2014)

  6. Gadelha Jr., L.M.R., et al.: A survey of biodiversity informatics: concepts, practices, and challenges. Wiley Interdiscip. Rev. Data Min. Knowl. Discov. 11(1), e1394 (2021)

    Google Scholar 

  7. Löffler, F., Abdelmageed, N., Babalou, S., Kaur, P., König-Ries, B.: Tag me if you can! Semantic annotation of biodiversity metadata with the QEMP corpus and the BiodivTagger. In: Proceedings of The 12th Language Resources and Evaluation Conference, pp. 4557–4564 (2020)

    Google Scholar 

  8. Pedersen, T., Patwardhan, S., Michelizzi, J., et al.: WordNet: similarity-measuring the relatedness of concepts. AAAI 4, 25–29 (2004)

    Google Scholar 

  9. Pinto, H.S., Martins, J.P.: Ontologies: how can they be built? Knowl. Inf. Syst. 6(4), 441–464 (2004)

    Article  Google Scholar 

  10. Scherp, A., Saathoff, C., Franz, T., Staab, S.: Designing core ontologies. Appl. Ontol. 6(3), 177–221 (2011)

    Article  Google Scholar 

  11. Udovenko, V., Algergawy, A.: Entity extraction in the ecological domain-a practical guide. BTW 2019-Workshopband (2019)

    Google Scholar 

Download references

Acknowledgments

The authors thank the Carl Zeiss Foundation for the financial support of the project “A Virtual Werkstatt for Digitization in the Sciences (K3, P5)” within the scope of the program line “Breakthroughs: Exploring Intelligent Systems” for “Digitization - explore the basics, use applications”. Alsayed Algergawy’ work has been funded by the Deutsche Forschungsgemeinschaft (DFG) as part of CRC 1076 AquaDiva. Our sincere thanks to Tina Heger (Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB)) as the domain expert.

Author information

Authors and Affiliations

  1. Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Jena, Germany

    Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel & Birgitta König-Ries

  2. Computer Vision Group, Friedrich Schiller University Jena, Jena, Germany

    Nora Abdelmageed

  3. Michael Stifel Center Jena, Friedrich Schiller University Jena, Jena, Germany

    Nora Abdelmageed, Sheeba Samuel & Birgitta König-Ries

Authors
  1. Nora Abdelmageed
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alsayed Algergawy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sheeba Samuel
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Birgitta König-Ries
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nora Abdelmageed .

Editor information

Editors and Affiliations

  1. IMEC, Ghent University, Ghent, Belgium

    Ruben Verborgh

  2. Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium

    Anastasia Dimou

  3. University of Chile, Santiago, Chile

    Aidan Hogan

  4. Università degli Studi di Bari, Bari, Italy

    Claudia d'Amato

  5. Faculty of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Ilaria Tiddi

  6. Corporate Technology, Siemens Aktiengesellschaft, München, Bayern, Germany

    Arne Bröring

  7. University of St. Gallen, St. Gallen, St. Gallen, Switzerland

    Simon Mayer

  8. Ghent University, Ghent, Belgium

    Femke Ongenae

  9. Institute of Computer Science, University of Tartu, Tartu, Estonia

    Riccardo Tommasini

  10. Information Infrastructure, FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany

    Mehwish Alam

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Abdelmageed, N., Algergawy, A., Samuel, S., König-Ries, B. (2021). BiodivOnto: Towards a Core Ontology for Biodiversity. In: Verborgh, R., et al. The Semantic Web: ESWC 2021 Satellite Events. ESWC 2021. Lecture Notes in Computer Science(), vol 12739. Springer, Cham. https://doi.org/10.1007/978-3-030-80418-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-80418-3_1

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-80417-6

  • Online ISBN: 978-3-030-80418-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation