BioGrakn: A Knowledge Graph-Based Semantic Database for Biomedical Sciences

  • Antonio Messina
  • Haikal Pribadi
  • Jo Stichbury
  • Michelangelo Bucci
  • Szymon Klarman
  • Alfonso Urso
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 611)

Abstract

The proliferation of biological research data generated and shared openly online is of huge benefit to the scientific community, but there are often significant challenges to overcome before it can be integrated from different sources and re-used to gain new knowledge. This paper introduces BioGrakn, which is a graph-based deductive database, combining the power of knowledge graphs and machine reasoning. BioGrakn illustrates how data can be aggregated and integrated, modelled in all its complexity and contextual specificity, and extended as needed. Built upon GRAKN.AI, it provides an integrated, intelligent database for researchers handling complex data.

Keywords

Knowledge representation and reasoning Semantic web Semantic data integration Biomedical Databases Knowledge graphs 

References

  1. 1.
    Cheung, K.H., Smith, A.K., Yip, K.Y., Baker, C.J., Gerstein, M.B.: Semantic web approach to database integration in the life sciences. In: Semantic Web. Springer, US (2007)Google Scholar
  2. 2.
    Have, C.T., Jensen, L.J.: Are graph databases ready for bioinformatics? Bioinformatics 29(24), 3107–3108 (2013)CrossRefGoogle Scholar
  3. 3.
    Bonnici, V., Russo, F., Bombieri, N., Pulvirenti, A., Giugno, R.: Comprehensive reconstruction and visualization of non-coding regulatory networks in human. Front. Bioeng. Biotechnol. 2, 69 (2014). doi:10.3389/fbioe.2014.00069 CrossRefGoogle Scholar
  4. 4.
    Pareja-Tobes, P., Tobes, R., Manrique, M., Pareja, E., Pareja-Tobes, E.: Bio4j: a high-performance cloud-enabled graph-based data platform. Era7 bioinformatics, Technical Report (2015)Google Scholar
  5. 5.
    Fiannaca, A., La Rosa, M., La Paglia, L., Messina, A., Urso, A.: BioGraphDB: a new GraphDB collecting heterogeneous data for bioinformatics analysis. In: BIOTECHNO 2016: The Eighth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies, Lisbon, Portugal, pp. 28–34 (2016)Google Scholar
  6. 6.
    Orient Technologies Ltd: OrientDB Community Edition. http://orientdb.com
  7. 7.
    Neo Technology Inc: Neo4J https://neo4j.com
  8. 8.
    Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D.B., Attwood, T.K.: Visualising biological data: a semantic approach to tool and database integration. BMC Bioinform. 10(6), S19 (2009)CrossRefGoogle Scholar
  9. 9.
    Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S.M., Martin, M., Le Novère, N., Parkinson, H., Birney, E., Jenkinson, A.M.: The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30, 1338–1339 (2014). (Oxford, England)CrossRefGoogle Scholar
  10. 10.
    Whetzel, P.L., Noy, N.F., Shah, N.H., Alexander, P.R., Nyulas, C., Tudorache, T., Musen, M.A.: BioPortal: enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications. Nucleic Acids Res. 39(Web Server issue), W541–W545 (2011)CrossRefGoogle Scholar
  11. 11.
    Cerami, E.G., Gross, B.E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G.D., Sander, C.: Pathway commons, a web resource for biological pathway data. Nucleic Acids Res. 39(Database issue), D685–D690 (2011)CrossRefGoogle Scholar
  12. 12.
    Pasquier, C.: Biological data integration using semantic web technologies. Biochimie 90(4), 584–594 (2008)CrossRefGoogle Scholar
  13. 13.
    Livingston, K.M., Bada, M., Baumgartner, W.A., Hunter, L.E.: KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinform. 16(1), 126 (2015)CrossRefGoogle Scholar
  14. 14.
    Grakn Labs Ltd: GRAKN.AI. https://grakn.ai
  15. 15.
    Schuler, G.D., Epstein, J.A., Ohkawa, H., Kans, J.A.: Entrez: molecular biology database and retrieval system. Methods Enzymol. 266, 141–162 (1996)CrossRefGoogle Scholar
  16. 16.
    The gene ontology consortium: gene ontology consortium: going forward. Nucleic Acids Res. 43(D1), 1049–1056 (2015)Google Scholar
  17. 17.
    The UniProt: a hub for protein information. Nucleic Acids Res. 43(D1), 204–212 (2015)Google Scholar
  18. 18.
    Croft, D., Mundo, A.F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M.R., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., D’Eustachio, P.: The reactome pathway knowledgebase. Nucleic Acids Res. 42(D1), 472–477 (2014)CrossRefGoogle Scholar
  19. 19.
    Kozomara, A., Griffiths-Jones, S.: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, 152–157 (2011). Database issueCrossRefGoogle Scholar
  20. 20.
    Xie, B., Ding, Q., Han, H., Wu, D.: miRCancer: a microRNA-cancer association database constructed by text mining on literature. Bioinformatics 29(5), 638–644 (2013)CrossRefGoogle Scholar
  21. 21.
    Gong, J., Tong, Y., Zhang, H.M., Wang, K., Hu, T., Shan, G., Sun, J., Guo, A.Y.: Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum. Mutat. 33(1), 254–263 (2012)CrossRefGoogle Scholar
  22. 22.
    Hsu, S.-D., Tseng, Y.-T., Shrestha, S., Lin, Y.-L., Khaleel, A., Chou, C.-H., Chu, C.-F., Huang, H.-Y., Lin, C.-M., Ho, S.-Y., Jian, T.-Y., Lin, F.-M., Chang, T.-H., Weng, S.-L., Liao, K.-W., Liao, I.-E., Liu, C.-C., Huang, H.-D.: miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 42(D1), 78–85 (2014)CrossRefGoogle Scholar
  23. 23.
    John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., Marks, D.S.: Human microRNA targets. PLoS Biol. 2(11), e363 (2004)CrossRefGoogle Scholar
  24. 24.
    Gray, K.A., Yates, B., Seal, R.L., Wright, M.W., Bruford, E.A.: Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 43(D1), 1079–1085 (2015)CrossRefGoogle Scholar
  25. 25.
    Baker, W., Van den Broek, A., Camon, E., Hingamp, P., Sterk, P., Stoesser, G., Tuli, M.A.: The EMBL nucleotide sequence database. Nucleic Acids Res. 28(1), 19–23 (2000)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Antonio Messina
    • 1
  • Haikal Pribadi
    • 2
  • Jo Stichbury
    • 2
  • Michelangelo Bucci
    • 2
  • Szymon Klarman
    • 2
  • Alfonso Urso
    • 1
  1. 1.ICAR-CNRPalermoItaly
  2. 2.Grakn Labs LtdLondonUK

Personalised recommendations