Annotation of Colorectal Cancer Data Using the UMLS Metathesaurus

  • Marcos Martínez
  • José M. Vázquez
  • Javier Pereira
  • Alejandro Pazos
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5178)


Reusing the data collected during an epidemiological study is a complex task. This is mainly due to the frequent utilization of traditional storage supports, as well as specific formats and/or terminologies which can make it difficult to integrate the gathered data with data from other information resources. Using terms from the UMLS Metathesaurus, we have annotated the data collected during the development of an epidemiological study of colorectal cancer funded by the US National Cancer Institute (NCI), which was carried out in Galicia, Spain. In our opinion, this annotation can facilitate integration of these data with data from other studies, allowing the future development of larger studies in a faster and more economical manner.


Ontologies Knowledge Management Cancer 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Bodenreider, O.: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Research 32, 267–270 (2004)CrossRefGoogle Scholar
  2. 2.
    Vazquez, J.M., Martinez, M., Lopez, M.G., Gonzalez-Conde, B., Arnal, F.M., Pereira, J., Pazos, A.: Development of an Information System for Multicenter Epidemiologic Studies on Cancer, Tokio, Japan. Information Technology Applications in Biomedicine, 2007. ITAB 2007, pp. 149–152 (2007)Google Scholar
  3. 3.
    Pérez-Rey, D., Maojo, V., García-Remesal, M., Alonso-Calvo, R., Billhardt, H., Martin-Sánchez, F., Sousa, A.: ONTOFUSION: Ontology-based integration of genomic and clinical databases. Comput. Biol. Med. 36, 712–730 (2006)CrossRefGoogle Scholar
  4. 4.
    Barrasa, J., Corcho, O., Gómez-Pérez, A.: R2O, an Extensible and Semantically Based Database-to-Ontology Mapping Language. In: SWDB 2004 (2004)Google Scholar
  5. 5.
    Konstantinou, N., Spanos, D., Chalas, M., Solidakis, E., Mitrou, N.: VisAVis: An Approach to an Intermediate Layer between Ontologies and Relational Database Contents. In: Proc. Int. Workshop on Web Information Systems Modeling (2006)Google Scholar
  6. 6.
    Xu, Z., Zhang, S., Dong, Y.: Mapping between Relational Database Schema and OWL Ontology for Deep Annotation. In: Proceedings of the 2006 IEEE/WIC/ACM International Conference on Web Intelligence, pp. 548–552 (2006)Google Scholar
  7. 7.
    Shah, N.H., Rubin, D.L., Supekar, K.S., Musen, M.A.: Ontology-based Annotation and Query of Tissue Microarray Data. In: AMIA Annu. Symp. Proc., vol. 709, p. 13 (2006)Google Scholar
  8. 8.
    Wache, H., Vögele, T., Visser, U., Stuckenschmidt, H., Schuster, G., Neumann, H., Hübner, S.: Ontology-based integration of information-a survey of existing approaches. In: IJCAI-01 Workshop, pp. 108–117 (2001)Google Scholar
  9. 9.
    de Coronado, S., Haber, M.W., Sioutos, N., Tuttle, M.S., Wright, L.W.: NCI Thesaurus: Using Science-based Terminology to Integrate Cancer Research Results. Med. info. 11, 33–37 (2004)Google Scholar
  10. 10.
    Pisanelli, D.M., Gangemi, A., Steve, G.: An Ontological Analysis of the UMLS Metathesaurus. In: Proc. AMIA Symp., vol. 810, p. 4 (1998)Google Scholar
  11. 11.
    Maojo, V., Crespo, J., de la Calle, G., Barreiro, J., Garcia-Remesal, M.: Using Web Services for Linking Genomic Data to Medical Information Systems. Methods of Information in Medicine 46, 484–492 (2007)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Marcos Martínez
    • 1
  • José M. Vázquez
    • 1
  • Javier Pereira
    • 1
  • Alejandro Pazos
    • 1
  1. 1.IMEDIR CenterUniversity of A CoruñaSpain

Personalised recommendations