Skip to main content
SpringerLink
Log in

Biomolecular Annotation Integration and Querying to Help Unveiling New Biomedical Knowledge

  • Conference paper
  • First Online:
Bioinformatics and Biomedical Engineering (IWBBIO 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9656))

Included in the following conference series:

Abstract

Targeting biological questions requires comprehensive evaluation of multiple types of annotations describing current biological knowledge; they are increasingly available, but their fast evolution, heterogeneity and dispersion in many different sources hamper their effective use. Leveraging on innovative flexible data schema and automatic software procedures that support the integration of data sources evolving in number, data content and structure, while assuring quality and provenance tracking of the integrated data, we created a multi-organism Genomic and Proteomic Knowledge Base (GPKB) and easily maintained it updated. From several well-known databases it imports and integrates very numerous gene and protein data, external references and annotations, expressed through multiple biomedical terminologies. To easily query such integrated data, we developed intuitive web interfaces and services for programmatic access to the GPKB; they are publicly available respectively at http://www.bioinformatics.deib.polimi.it/GPKB/ and http://www.bioinformatics.deib.polimi.it/GPKB-REST/. The created GPKB is a very valuable resource used in several projects by many users; the developed interfaces enhance its relevance to the community by allowing the seamlessly composition of queries, although complex, on all data integrated in the GPKB, which can help unveiling new biomedical knowledge.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
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

References

  1. Galperin, M.Y., Rigden, D.J., Fernández-Suárez, X.M.: The 2015 nucleic acids research database issue and molecular biology database collection. Nucleic Acids Res. 43(Database issue), D1–D5 (2015)

    Article  Google Scholar 

  2. Sujansky, W.: Heterogeneous database integration in biomedicine. J. Biomed. Inform. 34(4), 285–298 (2001)

    Article  Google Scholar 

  3. Hernandez, T., Kambhampati, S.: Integration of biological sources: current systems and challenges ahead. ACM Sigmod Rec. 33(3), 51–60 (2004)

    Article  Google Scholar 

  4. Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G., Kasprzyk, A.: BioMart - Biological queries made easy. BMC Genom. 10(1), 22 (2009)

    Article  Google Scholar 

  5. Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., et al.: TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. Bioinform. 16(2), 184–185 (2000)

    Article  Google Scholar 

  6. Freier, A., Hofestädt, R., Lange, M., Scholz, U., Stephanik, A.: BioDataServer: a SQL-based service for the online integration of life science data. Silico Biol. 2(2), 37–57 (2002)

    Google Scholar 

  7. Cadag, E., Louie, B., Myler, P.J., Tarczy-Hornoch, P.: Biomediator data integration and inference for functional annotation of anonymous sequences. In: Pacific Symposium on Biocomputing, pp. 343–354 (2007)

    Google Scholar 

  8. Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W., Tenenbaum, J.D., Karp, P.D.: BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinform. 7, 170 (2006)

    Article  Google Scholar 

  9. Birkland, A., Yona, G.: BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinform. 7, 70 (2006)

    Article  Google Scholar 

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

    Article  Google Scholar 

  11. Louie, B., Mork, P., Martin-Sanchez, F., Halevy, A., Tarczy-Hornoch, P.: Data integration and genomic medicine. J. Biomed. Inform. 40(1), 5–16 (2007)

    Article  Google Scholar 

  12. Goble, C., Stevens, R.: State of the nation in data integration for bioinformatics. J. Biomed. Inform. 41(5), 687–693 (2008)

    Article  Google Scholar 

  13. Lapatas, V., Stefanidakis, M., Jimenez, R.C., Via, A., Schneider, M.V.: Data integration in biological research: an overview. J. Biol. Res. (Thessalon) 22(1), 9 (2015)

    Article  Google Scholar 

  14. Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., et al.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Syst. J. 40(2), 512–531 (2001)

    Article  Google Scholar 

  15. Bornberg-Bauer, E., Paton, N.W.: Conceptual data modelling for bioinformatics. Brief. Bioinform. 3(2), 166–180 (2002)

    Article  Google Scholar 

  16. Masseroli, M., Ceri, S., Campi, A.: Integration and mining of genomic annotations: experiences and perspectives in GFINDer data warehousing. In: Paton, N.W., Missier, P., Hedeler, C. (eds.) DILS 2009. LNCS, vol. 5647, pp. 88–95. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  17. Canakoglu, A., Masseroli, M., Ceri, S., Tettamanti, L., Ghisalberti, G., Campi, A.: Integrative warehousing of biomolecular information to support complex multi-topic queries for biomedical knowledge discovery. In: Nikita, S.K., Fotiadis, D.I., (eds.) Proceedings of Thirteenth IEEE International Conference Bioinformatics and Bioengineering, (BIBE 2013), vol. 159, pp.1–4. IEEE Computer Society, Los Alamitos, CA (2013)

    Google Scholar 

  18. Ghisalberti, G., Masseroli, M., Tettamanti, L.: Quality controls in integrative approaches to detect errors and inconsistencies in biological databases. J. Integr. Bioinform. 7(3), 119, 1–13 (2010)

    Google Scholar 

  19. Masseroli, M., Canakoglu, A., Quigliatti, M.: Detection of gene annotations and protein-protein interaction associated disorders through transitive relationships between integrated annotations. BMC Genom. 16(Suppl 6), S5 (2015)

    Article  Google Scholar 

  20. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., et al.: Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15(10), 1451–1455 (2005)

    Article  Google Scholar 

  21. Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D., Owen, S., et al.: The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 41(Web Server issue), W557–W561 (2013)

    Article  Google Scholar 

  22. LinkingOpenData W3C SWEO community project. http://www.w3.org/wiki/SweoIG/TaskForces/CommunityProjects/LinkingOpenData. Accessed 01 December 2015

  23. Samwald, M., Jentzsch, A., Bouton, C., Kallesøe, C.S., Willighagen, E., Hajagos, J., et al.: Linked open drug data for pharmaceutical research and development. J. Cheminform. 3(1), 19 (2011)

    Article  Google Scholar 

  24. Masseroli, M., Picozzi, M., Ghisalberti, G., Ceri, S.: Explorative search of distributed bio-data to answer complex biomedical questions. BMC Bioinform. 15(Suppl 1): S3, 1–14 (2014)

    Google Scholar 

  25. Cohen, T., Widdows, D., Schvaneveldt, R.W., Davies, P., Rindflesch, T.C.: Discovering discovery patterns with predication-based semantic indexing. J. Biomed. Inform. 45(6), 1049–1065 (2012)

    Article  Google Scholar 

  26. Kilicoglu, H., Shin, D., Fiszman, M., Rosemblat, G., Rindflesch, T.C.: SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinform. 28(23), 3158–3160 (2012)

    Article  Google Scholar 

Download references

Acknowledgements

The authors would like to thank the several students who co-worked on developing and making publicly available the GPKB and its web and service interfaces, particularly Maria Carucci, Vincenzo Di Girolamo, Stefano Gennaro, and Marta Morfina.

Author information

Authors and Affiliations

  1. Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy

    Arif Canakoglu, Stefano Ceri & Marco Masseroli

Authors
  1. Arif Canakoglu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stefano Ceri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marco Masseroli
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marco Masseroli .

Editor information

Editors and Affiliations

  1. Universidad de Granada, Granada, Spain

    Francisco Ortuño

  2. Universidad de Granada, Granada, Spain

    Ignacio Rojas

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this paper

Cite this paper

Canakoglu, A., Ceri, S., Masseroli, M. (2016). Biomolecular Annotation Integration and Querying to Help Unveiling New Biomedical Knowledge. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2016. Lecture Notes in Computer Science(), vol 9656. Springer, Cham. https://doi.org/10.1007/978-3-319-31744-1_69

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-31744-1_69

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-31743-4

  • Online ISBN: 978-3-319-31744-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation