Skip to main content
SpringerLink
Log in

Training Biomedical Researchers in Metadata with a MIBBI-Based Ontology

  • Conference paper
  • First Online:
Metadata and Semantic Research (MTSR 2019)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1057))

Included in the following conference series:

Abstract

Recent initiatives in data management recognize that involving the researchers is one of the more problematic issues and that taking into account the practices of each domain can ease this process. We describe here an experiment in the adoption of data description by researchers in the biomedical domain. We started with a generic lightweight ontology based on the Minimum Information for Biological and Biomedical Investigations (MIBBI) standard and presented it to researchers from the Institute of Innovation and Investigation in Health (I3S) in Porto. This resulted in seven interviews and four data description sessions using a RDM platform. The feedback from researchers shows that this intentionally restricted ontology favours an easy entry point into RDM but does not prevent them from identifying the limitations of the model and pinpointing their specific domain requirements. To complete the experiment, we collected the extra descriptors suggested by the researchers and compared them to the full MIBBI. Part of these new descriptors can be obtained from the standard, reinforcing the importance of common metadata models for broad domains such as biomedical research.

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

Access this chapter

Log in via an institution
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 shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    http://rd-alliance.github.io/metadata-directory/standards/.

  2. 2.

    http://www.dcc.ac.uk/resources/standards/.

  3. 3.

    https://docs.patricbrc.org/user_guides/organisms_taxon/genome_metadata.html.

  4. 4.

    https://fairsharing.org/collection/MIBBI.

  5. 5.

    http://www.obofoundry.org/.

  6. 6.

    http://bioportal.bioontology.org/.

  7. 7.

    http://protege.stanford.edu/.

  8. 8.

    http://www.dublincore.org/specifications/dublin-core/dces/.

References

  1. Assante, M., et al.: Are scientific data repositories coping with research data publishing? Data Sci. J. 15(6), 1–24 (2016). https://doi.org/10.5334/dsj-2016-006. ISSN 1683-1470

    Article  Google Scholar 

  2. Bandrowski, A., et al.: The ontology for biomedical investigations. PLoS ONE 11(4), 1–19 (2016)

    Article  Google Scholar 

  3. Brazma, A., et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29(4), 365 (2001)

    Article  Google Scholar 

  4. Castro, J.A., et al.: Involving data creators in an ontology-based design process for metadata models. In: Developing Metadata Application Profiles, pp. 181–213 (2017).https://doi.org/10.1007/s00799-018-0238-x

    Article  Google Scholar 

  5. Cech, T.R.: Fostering innovation and discovery in biomedical research. JAMA 294(11), 1390–1393 (2005)

    Article  Google Scholar 

  6. Directorate-General for Research and Innovation (European Commission). Turning FAIR into reality. Technical report, pp. 1–78 (2018). https://doi.org/10.2777/1524

  7. González-Beltrán, A., et al.: linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinform. 15(14), S4 (2014)

    Article  Google Scholar 

  8. Hey, A.J.G., Tansley, S., Tolle, K.M., et al.: The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research (2009). ISBN 978-0-9825442-0-4

    Google Scholar 

  9. Hoehndorf, R., Schofield, P.N., Gkoutos, G.V.: The role of ontologies in biological and biomedical research: a functional perspective. Brief. Bioinform. 16(6), 1069–1080 (2015). https://doi.org/10.1093/bib/bbv011

    Article  Google Scholar 

  10. Mayer, G., et al.: Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim. Biophys. Acta (BBA) - Proteins Proteomics 1844(1), 98–107 (2014). https://doi.org/10.1016/j.bbapap.2013.02.017

    Article  Google Scholar 

  11. Qin, J., Ball, A., Greenberg, J.: Functional and architectural requirements for metadata: supporting discovery and management of scientific data. In: Proceedings of the International Conference on Dublin Core and Metadata Applications, pp. 62–71 (2012). ISSN 1939-1366. https://doi.org/10.1007/s00799-013-0106-7

    Article  Google Scholar 

  12. Read, K.: Common Metadata Elements for Cataloging Biomedical Datasets. https://doi.org/10.6084/m9.figshare.1496573.v1

  13. Sansone, S.-A., et al.: FAIRsharing as a community approach to standards, repositories and policies. Nat. Biotechnol. 37(4), 358 (2019)

    Article  Google Scholar 

  14. da Silva, J.R., Ribeiro, C., Lopes, J.C.: Ranking Dublin Core descriptor lists from user interactions: a case study with Dublin Core terms using the Dendro platform. Int. J. Digit. Libr. 20(2) (2019). https://doi.org/10.1007/s00799-018-0238-x

    Article  Google Scholar 

  15. Taylor, C.F., et al.: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol. 26(8), 889–896 (2009). https://doi.org/10.1038/nbt.1411.Promoting

    Article  Google Scholar 

  16. Taylor, C.F., et al.: The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25(8), 887–893 (2007)

    Article  Google Scholar 

  17. Tenopir, C., et al.: Changes in data sharing and data reuse practices and perceptions among scientists worldwide. PLoS ONE 10(8), 26–40 (2015). ISSN 1613-0073. https://doi.org/10.1371/journal.pone.0134826

    Article  Google Scholar 

  18. Wilkinson, M.D., et al.: The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3 (2016). https://doi.org/10.1038/sdata.2016.18

  19. Willis, C., Greenberg, J., White, H.: Analysis and synthesis of metadata goals for scientific data. J. Am. Soc. Inf. Sci. Technol. 63(8), 1505–1520 (2012). https://doi.org/10.1002/asi

    Article  Google Scholar 

  20. Willoughby, C., et al.: Creating context for the experiment record. User-defined metadata: investigations into metadata usage in the LabTrove ELN. J. Chem. Inf. Model. 54, 3268–3283 (2014). https://doi.org/10.1021/ci500469f

    Article  Google Scholar 

Download references

Acknowledgements

This work is financed by the ERDF – European Regional Development Fund through the Operational Programme for Competitiveness and Internationalisation - COMPETE 2020 Programme and by National Funds through the Portuguese funding agency, FCT - Fundação para a Ciência e a Tecnologia within project TAIL, POCI-01-0145-FEDER-016736. João Aguiar Castro is supported by research grant PD/BD/114143/2015, provided by the FCT - Fundação para a Ciência e a Tecnologia.

Author information

Authors and Affiliations

  1. INESC TEC, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal

    Marcelo Sampaio, Ana Luís Ferreira, João Aguiar Castro & Cristina Ribeiro

Authors
  1. Marcelo Sampaio
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ana Luís Ferreira
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. João Aguiar Castro
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cristina Ribeiro
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to João Aguiar Castro .

Editor information

Editors and Affiliations

  1. International Hellenic University, Thessaloniki, Greece

    Emmanouel Garoufallou

  2. Guglielmo Marconi University, Rome, Italy

    Francesca Fallucchi

  3. Georg Eckert Institute – Leibniz Institute for International Textbook Research, Braunschweig, Germany

    Ernesto William De Luca

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Sampaio, M., Ferreira, A.L., Castro, J.A., Ribeiro, C. (2019). Training Biomedical Researchers in Metadata with a MIBBI-Based Ontology. In: Garoufallou, E., Fallucchi, F., William De Luca, E. (eds) Metadata and Semantic Research. MTSR 2019. Communications in Computer and Information Science, vol 1057. Springer, Cham. https://doi.org/10.1007/978-3-030-36599-8_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-36599-8_3

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-36598-1

  • Online ISBN: 978-3-030-36599-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation