BioMed Xplorer - Exploring (Bio)Medical Knowledge using Linked Data

Mohammad Shafahi, Hayo Bart, Hamideh Afsarmanesh


Developing an effective model for predicting risks of a disease requires exploration of a vast body of (bio)medical knowledge. Furthermore, the continuous growth of this body of knowledge poses extra challenges. Numerous research has attempted to address these issues through developing a variety of approaches and support tools. Most of these tools however, do not sufficiently address the needed dynamism, lack intuitiveness in their use, and present a rather scarce amount of information usually obtained from a single source. This research aims to address the aforementioned gaps through the development of a dynamic model for (bio)medical knowledge, represented as a network of interrelated (bio)medical concepts, and integrating disperse sources. To this end, this paper introduces BioMed Xplorer, presenting a model and a tool that enables researchers to explore biomedical knowledge, organized in an information graph, through a user friendly and intuitive interface. Furthermore, BioMed Xplorer provides concept related information from a multitude of sources, while also preserving and presenting their provenance data. For this purpose a RDF knowledge base has been created based on a core ontology which we have introduced. Results are further experimented with and validated by some domain experts and are contrasted against the state of the art.


  1. Antoniou, G. and Van Harmelen, F. (2004). A semantic web primer. MIT press.
  2. 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., et al. (2000). Gene ontology: tool for the unification of biology. Nature genetics, 25(1):25-29.
  3. Belleau, F., Nolin, M.-A., Tourigny, N., Rigault, P., and Morissette, J. (2008). Bio2rdf: towards a mashup to build bioinformatics knowledge systems. Journal of biomedical informatics, 41(5):706-716.
  4. Berners-Lee, T., Bizer, C., and Heath, T. (2009). Linked data-the story so far. International Journal on Semantic Web and Information Systems, 5(3):1-22.
  5. Berners-Lee, T., Hendler, J., Lassila, O., et al. (2001). The semantic web. Scientific american , 284(5):28-37.
  6. Bizer, C. and Cyganiak, R. (2006). D2r server-publishing relational databases on the semantic web. In Poster at the 5th International Semantic Web Conference, pages 294-309.
  7. Bizer, C. and Seaborne, A. (2004). D2rq-treating nonrdf databases as virtual rdf graphs. In Proceedings of the 3rd international semantic web conference (ISWC2004), volume 2004. Citeseer Hiroshima.
  8. Bodenreider, O. (2000). A semantic navigation tool for the umls. In Proceedings of the AMIA Symposium, page 971. American Medical Informatics Association.
  9. Cohen, A. M. and Hersh, W. R. (2005). A survey of current work in biomedical text mining. Briefings in bioinformatics, 6(1):57-71.
  10. D'Arcus, B. and Giasson, F. (2015). ographic Ontology Specification accessed August 28 2015].
  11. Dean, M., Schreiber, G., Bechhofer, S., van Harmelen, F., Hendler, J., Horrocks, I., McGuinness, D. L., PatelSchneider, P. F., and Stein, L. A. (2004). Owl web ontology language reference. W3C Recommendation February, 10.
  12. Dublin Core Metadata Initiative (DCMI) (2015). Dublin Core (DC). [Online; accessed August 28 2015].
  13. Harris, S., Seaborne, A., and Prudhommeaux, E. (2013). Sparql 1.1 query language. W3C Recommendation, 21.
  14. Hendler, J. (2014). Data integration for heterogenous datasets. Big data, 2(4):205-215.
  15. Hunter, L. and Cohen, K. B. (2006). Biomedical language processing: what's beyond pubmed? Molecular cell, 21(5):589-594.
  16. Institute for Genome Sciences - University of Maryland School of Medicine (2015). Disease Ontology (DO). [Online; accessed August 28 2015].
  17. Institute of Applied Informatics and Formal Description Methods - Karlsruhe Research Institute (2015). [Online; accessed August 28 2015].
  18. International Health Terminology Standards Development Organisation (2015). Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). [Online; accessed August 28 2015].
  19. Johns Hopkins University (2015). Online Mendelian Inheritance in Man (OMIM). [Online; accessed August 28 2015].
  20. Kilicoglu, H., Fiszman, M., Rodriguez, A., Shin, D., Ripple, A., and Rindflesch, T. C. (2008). Semantic medline: a web application for managing the results of pubmed searches. In Proceedings of the third international symposium for semantic mining in biomedicine, volume 2008, pages 69-76. Citeseer.
  21. Kilicoglu, H., Shin, D., Fiszman, M., Rosemblat, G., and Rindflesch, T. C. (2012). Semmeddb: a pubmedscale repository of biomedical semantic predications. Bioinformatics, 28(23):3158-3160.
  22. Lu, Z. (2011). Pubmed and beyond: a survey of web tools for searching biomedical literature. Database, 2011:baq036.
  23. Momtchev, V., Peychev, D., Primov, T., and Georgiev, G. (2009). Expanding the pathway and interaction knowledge in linked life data. Proc. of International Semantic Web Challenge.
  24. Plake, C., Schiemann, T., Pankalla, M., Hakenberg, J., and Leser, U. (2006). Alibaba: Pubmed as a graph. Bioinformatics, 22(19):2444-2445.
  25. Rebholz-Schuhmann, D., Kirsch, H., Arregui, M., Gaudan, S., Riethoven, M., and Stoehr, P. (2007). Ebimedtext crunching to gather facts for proteins from medline. Bioinformatics, 23(2):e237-e244.
  26. Shadbolt, N., Hall, W., and Berners-Lee, T. (2006). The semantic web revisited. Intelligent Systems, IEEE, 21(3):96-101.
  27. Tao, C., Zhang, Y., Jiang, G., Bouamrane, M.-M., and Chute, C. G. (2012). Optimizing semantic medline for translational science studies using semantic web technologies. In Proceedings of the 2nd international workshop on Managing interoperability and compleXity in health systems, pages 53-58. ACM.
  28. Tao, Y., Friedman, C., and Lussier, Y. A. (2005). Visualizing information across multidimensional postgenomic structured and textual databases. Bioinformatics, 21(8):1659-1667.
  29. U.S. National Cancer Institute (2015a). NCI Metathesaurus (NCIm). [Online; accessed August 28 2015].
  30. U.S. National Cancer Institute (2015b). NCI Thesaurus (NCIt). [Online; accessed August 28 2015].
  31. National Library of Medicine (2015a).
  32. [Online; accessed August 28 2015]. National Library of Medicine
  33. (2015b). Medline fact sheet.
  34. [Online; accessed August 28 2015].
  35. U.S. National Library of Medicine (2015c). Medline Plus. [Online; accessed August 28 2015].
  36. U.S. National Library of Medicine (2015d). SemRep. [Online; accessed August 28 2015].
  37. U.S. National Library of Medicine (2015e). Unified Medical Language System (UMLS). [Online; accessed August 28 2015].
  38. WebMD, LLC (2015). WebMD. [Online; accessed August 28 2015].
  39. Weibel, S. L., Jul, E., and Shafer, K. E. (1996). PURLs: Persistent uniform resource locators. OCLC Online Computer Library Center.
  40. Weizmann Institute of Science (2015). MalaCards. [Online; accessed August 28 2015].
  41. World Health Organization (2015). International Classification of Diseases (ICD). [Online; accessed August 28 2015].
  42. World Wide Web Consortium (2015). Simple Knowledge Organization System (SKOS). [Online; accessed August 28 2015].
  43. World Wide Web Consortium et al. (2014). Rdf 1.1 semantics.

Paper Citation

in Harvard Style

Shafahi M., Bart H. and Afsarmanesh H. (2016). BioMed Xplorer - Exploring (Bio)Medical Knowledge using Linked Data . In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 51-62. DOI: 10.5220/0005700300510062

in Bibtex Style

author={Mohammad Shafahi and Hayo Bart and Hamideh Afsarmanesh},
title={BioMed Xplorer - Exploring (Bio)Medical Knowledge using Linked Data},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)},

in EndNote Style

JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)
TI - BioMed Xplorer - Exploring (Bio)Medical Knowledge using Linked Data
SN - 978-989-758-170-0
AU - Shafahi M.
AU - Bart H.
AU - Afsarmanesh H.
PY - 2016
SP - 51
EP - 62
DO - 10.5220/0005700300510062