Skip to main content
SpringerLink
Log in

SCALEUS: Semantic Web Services Integration for Biomedical Applications

  • Systems-Level Quality Improvement
  • Published:
Journal of Medical Systems Aims and scope Submit manuscript

Abstract

In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. van Dijk, E.L., Auger, H., Jaszczyszyn, Y., and Thermes, C., Ten years of next-generation sequencing technology. Trends Genet. 30(9):418–426, 2014.

    Article  PubMed  Google Scholar 

  2. Gomez-Cabrero, D., Abugessaisa, I., Maier, D., Teschendorff, A., Merkenschlager, M., Gisel, A., Ballestar, E., Bongcam-Rudloff, E., Conesa, A., and Tegnér, J., Data integration in the era of omics: current and future challenges. BMC Syst. Biol. 8(Suppl 2):I1, 2014.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Berners-Lee, T., Hendler, J., and Lassila, O., The semantic web. Sci. Am. 284(5):28–37, 2001.

    Article  Google Scholar 

  4. Passin, T., Explorer’s guide to the semantic web, 2004.

  5. Machado, C.M., Rebholz-Schuhmann, D., Freitas, A.T., and Couto, F.M., The semantic web in translational medicine: current applications and future directions. Brief. Bioinform. 16(1):89–103, 2015.

    Article  PubMed  Google Scholar 

  6. Belleau, F., Nolin, M.-A., Tourigny, N., Rigault, P., and Morissette, J., Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41(5):706–716, 2008.

    Article  PubMed  Google Scholar 

  7. Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., and Redaschi, N., The EBI RDF platform: linked open data for the life sciences. Bioinformatics. 30(9):1338–1339, 2014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sernadela, P., Lopes, P., and Oliveira, J.L., A knowledge federation architecture for rare disease patient registries and biobanks. J. Inf. Syst. Eng. Manag. 1(1):83–90, 2016.

    Google Scholar 

  9. Freitas, A., Curry, E., Oliveira, J.G., and O’Riain, S., Querying heterogeneous datasets on the linked data web: challenges, approaches, and trends. IEEE Internet Comput. 16(1):24–33, 2012.

    Article  Google Scholar 

  10. J. Pathak, R. Kiefer, and C. Chute, Using semantic web technologies for cohort identification from electronic health records for clinical research. AMIA Summits Transl. Sci. Proc. 2012, 2012.

  11. C. David, C. Olivier, and B. Guillaume, A survey of RDF storage approaches. ARIMA J., 2012.

  12. O. Erling, Virtuoso, a hybrid RDBMS/graph column store. IEEE Data Eng. Bull., 2012.

  13. Lopes, P., and Oliveira, J.L., COEUS: ‘semantic web in a box’ for biomedical applications. J. Biomed. Semantics. 3(1):11, 2012.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Broekstra, J., Kampman, A., and Van Harmelen, F., Sesame: A generic architecture for storing and querying rdf and rdf schema. Semant. Web — ISWC 2002. 2342:54–68, 2002.

    Article  Google Scholar 

  15. Aasman, J., Allegro graph: RDF triple database. Franz Inc., Cid. Oakl, 2006.

    Google Scholar 

  16. G. E. Modoni, M. Sacco, and W. Terkaj, A survey of RDF store solutions. In 2014 International conference on engineering, Technology and Innovation: Engineering Responsible Innovation in Products and Services, ICE 2014, 2014.

  17. Gurupur, V.P., and Tanik, M.M., A system for building clinical research applications using semantic web-based approach. J. Med. Syst. 36(1):53–59, 2012.

    Article  PubMed  Google Scholar 

  18. E. Mezghani, E. Exposito, K. Drira, M. Da Silveira, and C. Pruski, A Semantic Big Data Platform for Integrating Heterogeneous Wearable Data in Healthcare. J. Med. Syst., vol. 39, no. 12, p. 185, 2015.

  19. C. Bizer, T. Heath, and T. Berners-Lee, Linked data-the story so far. Int. J. Semant. Web Inf. Syst., 2009.

  20. S. Schenk, P. Gearon, and A. Passant, SPARQL 1.1 Update. World Wide Web Consort., 2010.

  21. S. Harris, A. Seaborne, and E. Prud’hommeaux, SPARQL 1.1 query language. W3C Recomm. 21, 2013.

  22. C. Forgy, Rete: a fast algorithm for the many pattern/many object pattern match problem. Artif. Intell. 1982.

  23. Weibel, S., The Dublin Core: a simple content description model for electronic resources. Bull. Am. Soc. Inf. Sci. Technol. 24(1):9–11, 1997.

    Article  Google Scholar 

  24. R. Thompson, L. Johnston, D. Taruscio, L. Monaco, C. Béroud, I. G. Gut, M. G. Hansson, P.-B. A. ‘t Hoen, G. P. Patrinos, H. Dawkins, M. Ensini, K. Zatloukal, D. Koubi, E. Heslop, J. E. Paschall, M. Posada, P. N. Robinson, K. Bushby, and H. Lochmüller, “RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research. J. Gen. Intern. Med. 2014.

  25. Zollino, M., Ponzi, E., Gobbi, G., and Neri, G., The ring 14 syndrome. Eur. J. Med. Genet. 55(5):374–380, 2012.

    Article  PubMed  Google Scholar 

  26. Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L.B., Bourne, P.E., Bouwman, J., Brookes, A.J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C.T., Finkers, R., Gonzalez-Beltran, A., Gray, A.J.G., Groth, P., Goble, C., Grethe, J.S., Heringa, J., ‘t Hoen, P.A.T., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S.J., Martone, M.E., Mons, A., Packer, A.L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M.A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J., and Mons, B., The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 3:160018, 2016.

  27. Rath, A., Olry, A., Dhombres, F., Brandt, M.M., Urbero, B., and Ayme, S., Representation of rare diseases in health information systems: the orphanet approach to serve a wide range of end users. Hum. Mutat. 33(5):803–808, 2012.

    Article  PubMed  Google Scholar 

  28. Barrell, D., Dimmer, E., Huntley, R.P., Binns, D., O’Donovan, C., and Apweiler, R., The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 37(Database):D396–D403, 2009.

    Article  CAS  PubMed  Google Scholar 

  29. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25(1):25–29, May 2000.

    CAS  PubMed  Google Scholar 

  30. Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., and Yeh, L.-S.L., The Universal Protein Resource (UniProt). Nucleic Acids Res. 33(suppl_1):D154–D159, 2005.

    CAS  PubMed  Google Scholar 

  31. Kersey, P.J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R., The international protein index: an integrated database for proteomics experiments. Proteomics. 4(7):1985–1988, 2004.

    Article  CAS  PubMed  Google Scholar 

  32. C. Bizer and R. Cyganiak, D2r server-publishing relational databases on the semantic web. 5th Int. Semant. Web Conf., 2006.

  33. Pang, C., Sollie, A., Sijtsma, A., Hendriksen, D., Charbon, B., de Haan, M., de Boer, T., Kelpin, F., Jetten, J., van der Velde, J.K., Smidt, N., Sijmons, R., Hillege, H., and Swertz, M.A., SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. Database. 2015:bav089, 2015.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Campos, D., Lourenco, J., Matos, S., and Oliveira, J.L., Egas: a collaborative and interactive document curation platform. Database. 2014, 2014.

Download references

Author information

Authors and Affiliations

  1. DETI/IEETA, University of Aveiro, Campus Universitario de Santiago, Aveiro, 3810-193, Portugal

    Pedro Sernadela & José Luís Oliveira

  2. Galician Research and Development Center in Advanced Telecommunications (GRADIANT), Campus Universitario de Vigo, Vigo, 36310, Spain

    Lorena González-Castro

Authors
  1. Pedro Sernadela
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lorena González-Castro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. José Luís Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pedro Sernadela.

Ethics declarations

Funding

The research leading to these results has received funding from the European Community (FP7/2007–2013) under ref. no. 305444 – the RD-Connect project. Pedro Sernadela is funded by Fundação para a Ciência e Tecnologia (FCT) under the grant agreement SFRH/BD/52484/2014. Lorena González-Castro is funded by Xunta de Galicia, including funding from the operative program FSE Galicia 2007–2013, under the grant agreement IN809A 19/2015.

Conflict of Interest

All authors declare that there are no conflicts of interest in this work.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

This article is part of the Topical Collection on Systems-Level Quality Improvement

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sernadela, P., González-Castro, L. & Oliveira, J.L. SCALEUS: Semantic Web Services Integration for Biomedical Applications. J Med Syst 41, 54 (2017). https://doi.org/10.1007/s10916-017-0705-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10916-017-0705-8

Keywords

Search

Navigation