Skip to main content
SpringerLink
Log in

Integration of Genomic, Proteomic and Biomedical Information on the Semantic Web

  • Conference paper
Advances in Conceptual Modeling – Challenges and Opportunities (ER 2008)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 5232))

Included in the following conference series:

  • 1320 Accesses

Abstract

Researchers are faced with the challenge of integrating, on the basis of a common semantic web framework, the information on biological processes resulting from genomic and proteomic experimental studies. Researchers would like to integrate the biological processes’ roles in larger medical conditions, by taking account of the time dimension. This integration will support automated analysis and reasoning on the semantic web. We address these challenges by proposing the IGIPI framework, standing for “Integrating Gene Interactions and Protein Interactions”. IGIPI views different experimental studies as pieces of a puzzle that, if positioned properly, will contribute to a more complete representation of a biological process or medical condition over time. By representing the relative time points of events, this framework represents a biological process based on how it might be observed in an experiment over time. IGIPI involves integrating different ontologies and vocabularies, such as GO and UMLS/MeSH. We applied IGIPI to yeast and cancer examples. Availability: http://www.cse.yorku.ca/~billa/IGIPI/

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aranguren, M.E., Bechhofer, S., Lord, P., Sattler, U., Stevens, R.: Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 8, 57 (2007)

    Article  Google Scholar 

  2. Badea, L., Tilivea, D., Hotaran, A.: Semantic Web Reasoning for Ontology-Based Integration of Resources. In: Ohlbach, H.J., Schaffert, S. (eds.) PPSWR 2004. LNCS, vol. 3208, pp. 61–75. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  3. Brazhnik, O., Jones, J.F.: Anatomy of data integration. J Biomed Inform 40(3), 252–269 (2007); Epub 2006 (September 24, 2006)

    Article  Google Scholar 

  4. Burek, P., et al.: A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics 22(14), 66–73 (2006)

    Article  Google Scholar 

  5. Cheung, K.H., et al.: YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics 21 (suppl. 1), 85–96 (2005)

    Article  Google Scholar 

  6. Denecke, K.: Enhancing knowledge representations by ontological relations. Stud. Health Technol. Inform. 136, 791–796 (2008)

    Google Scholar 

  7. Dhanapalan, L., Chen, J.Y.: A case study of integrating protein interaction data using semantic web technology. Int. J. Bioinform. Res. Appl. 3(3), 286–302 (2007)

    Article  Google Scholar 

  8. Garcia-Sanchez, F., et al.: Combining Semantic Web technologies with Multi-Agent Systems for integrated access to biological resources. J. Biomed. Inform. (2008)

    Google Scholar 

  9. Koehler, J., Philippi, S., Lange, M.: SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19(18), 2420–2427 (2003)

    Article  Google Scholar 

  10. Lam, H., et al.: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 8 (suppl. 3), S4 (2007)

    Article  Google Scholar 

  11. Lam, H.Y., et al.: Using web ontology language to integrate heterogeneous databases in the neurosciences. In: AMIA Annu Symp Proc. 2006, pp. 464–468 (2006)

    Google Scholar 

  12. Marquet, G., Mosser, J., Burgun, A.: A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: the case of OBO disease ontologies. Int J Med Inform. 76 (suppl. 3), 353–361 (2007); Epub 2007 (May 22, 2007)

    Article  Google Scholar 

  13. Pasquier, C.: Biological data integration using Semantic Web technologies. Biochimie. 90(4), 584–594 (2008)

    Article  Google Scholar 

  14. Ruttenberg, A., et al.: Advancing translational research with the Semantic Web. BMC Bioinformatics 8 (suppl. 3), S2 (2007); Review

    Article  Google Scholar 

  15. Rubin, D.L., Shah, N.H., Noy, N.F.: Biomedical ontologies: a functional perspective. Brief Bioinform. 9(1), 75–90 (2008)

    Article  Google Scholar 

  16. Smith, A.K., Cheung, K.H., Yip, K.Y., Schultz, M., Gerstein, M.K.: LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinformatics 8 (suppl. 3), S5 (2007) Review

    Article  Google Scholar 

  17. Smith, A., Cheung, K., Krauthammer, M., Schultz, M., Gerstein, M.: Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinformatics 23(22), 3073–3079 (2007); Epub 2007 (October 7, 2007)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biotechnological Centre, Technische Universität Dresden Email: williama@biotec.tu-dresden.de, Germany

    Bill Andreopoulos & Dirk Labudde

  2. Dept. of Computer Science and Engineering, York University, Toronto, Canada

    Bill Andreopoulos, Aijun An & Xiangji Huang

Authors
  1. Bill Andreopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aijun An
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiangji Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dirk Labudde
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. College of Information Science and Technology, Drexel University, USA

    Il-Yeol Song

  2. Dep. of Information Technologies & Systems - Escuela Superior de Informática, University of Castilla-La Mancha, Alarcos Research Group- Institute of Information Technologies & Systems, Ciudad Real, Spain

    Mario Piattini

  3. School of Engineering and Information Technology, Deakin University, 221 Burwood Highway, Vic, 3125, Australia

    Yi-Ping Phoebe Chen

  4. Clausthal University of Technology, Julius-Albert-Str. 4, 38678, Clausthal-Zellerfeld, Germany

    Sven Hartmann

  5. Dipartimento di Elettronica, Informatica e Sistemistica, Alma Mater Studiorum – Università di Bologna, P.O. Box, Italy

    Fabio Grandi

  6. Department of Software and Computing Systems, University of Alicante, Spain

    Juan Trujillo

  7. Department of Information Science and Media Studies, University of Bergen, Fosswinckelsgate 6, 5007, Bergen, Norway

    Andreas L. Opdahl

  8. Istituto di Ricerche sulla Popolazione e Politiche Sociali, CNR, Via Nizza 128, 00198, Roma, Italy

    Fernando Ferri  & Patrizia Grifoni  & 

  9. IRPPS-CNR, Rome, Italy

    Maria Chiara Caschera

  10. Universit Paris1 Panthon Sorbonne, CRI, 90 Rue de Tolbiac, 75013, Paris

    Colette Rolland

  11. Portland State University, USA; Indiana University, USA University of British Columbia, Canada; Hill-Rom Company, USA University of British Columbia, Canada; Deloitte Consulting, P.O. Box, USA

    Carson Woo

  12. Centre de Recherche en Informatique, Université Paris 1 Panthéon-Sorbonne, 90 rue de Tolbiac, 75013, Paris

    Camille Salinesi

  13. Université Libre de Bruxelles, Belgium

    Esteban Zimányi

  14. Naval Academy Research Institute, Brest Naval, France

    Christophe Claramunt

  15. Technische Universiteit Eindhoven, PO Box 513, NL-5600 MB, Eindhoven, The Netherlands

    Flavius Frasincar

  16. Technische Universiteit Eindhoven, P.O. Box 513, NL 5600 MB, Eindhoven, The Netherlands

    Geert-Jan Houben

  17. IMRU-FUNDP, University of Namur, Namur, Belgium

    Philippe Thiran

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Andreopoulos, B., An, A., Huang, X., Labudde, D. (2008). Integration of Genomic, Proteomic and Biomedical Information on the Semantic Web. In: Song, IY., et al. Advances in Conceptual Modeling – Challenges and Opportunities. ER 2008. Lecture Notes in Computer Science, vol 5232. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87991-6_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-87991-6_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87990-9

  • Online ISBN: 978-3-540-87991-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation