BioGraphBot: A Conversational Assistant for Bioinformatics Graph Databases

  • Antonio Messina
  • Agnese Augello
  • Giovanni Pilato
  • Riccardo Rizzo
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 612)

Abstract

Chatbots technology allows to easily add a conversational interface to a large set of applications. In this paper, we show a conversational agent based on ALICE framework aimed at playing the role of interface between human users and a bioinformatics graph database. The system has been embedded into the web frontend of BioGraphDB, a publicly available resource that uses Gremlin as the primary query language. To be successfully exploited, domain experts, such as biologists and bioinformaticians, should also have familiarity with that query language. The use of a chatbot allows translating queries expressed in natural language to queries expressed in Gremlin, simplifying the interaction with BioGraphDB.

Keywords

Chatbot Human computer interfaces Biomedical Databases NoSQL Gremlin 

References

  1. 1.
    Nihalani, N., Motwani, M., Silakari, S.: Natural language interface to database using semantic matching. Int. J. Comput. Appl. 31(11), 29–34 (2011)Google Scholar
  2. 2.
    Hoshino, A., Kato, K., Takeuchi, J., Tsujino, H.: A chat information service system using a humanoid robot. In: IEEE International Workshop on Robot and Human Interactive Communication, ROMAN 2005. IEEE (2005)Google Scholar
  3. 3.
    Androutsopoulos, I., Ritchie, G.D., Thanisch, P.: Natural language interfaces to databases - an introduction. Nat. Lang. Eng. 1(1), 29–81 (1995)CrossRefGoogle Scholar
  4. 4.
    Mahmud, T., Azharul, K.M., Ahmed, M., Chak, T.H.C.: A rule based approach for NLP based query processing. In: 2015 2nd International Conference on Electrical Information and Communication Technology (EICT). IEEE (2015)Google Scholar
  5. 5.
    Utami, D., Barry, B., Bickmore, T., Paasche-Orlow, M.: A conversational agent-based clinical trial search engine. In: Proceedings of the Annual Symposium on Human-Computer Interaction and Information Retrieval (HCIR), Vancouver, BC, Canada (2013)Google Scholar
  6. 6.
    Owda, M., Bandar, Z., Crockett, K.: Conversation-based natural language interface to relational databases. In: 2007 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology Workshops. IEEE (2007)Google Scholar
  7. 7.
    Fiannaca, A., La Rosa, M., La Paglia, L., Messina, A., Urso, A.: BioGraphDB: a new GraphDB collecting heterogeneous data for bioinformatics analysis. In: The Eighth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies, BIOTECHNO 2016, Lisbon, Portugal, pp. 28–34 (2016)Google Scholar
  8. 8.
    Rodriguez, M.A.: The Gremlin graph traversal machine and language (Invited Talk). In: Proceedings of the 15th Symposium on Database Programming Languages, DBPL 2015, pp. 1–10. ACM, New York (2015)Google Scholar
  9. 9.
    Apache Software Foundation: Apache Tinkerpop. http://tinkerpop.apache.org
  10. 10.
    Fiannaca, A., La Paglia, L., La Rosa, M., Messina, A., Rizzo, R., Stabile, D., Urso, A.: Gremlin language for querying BiographDB integrated biological database. In: 4th International Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2017, Granada, Spain (2017, in press)Google Scholar
  11. 11.
    Fiannaca, A., La Paglia, L., La Rosa, M., Messina, A., Storniolo, P., Urso, A.: Integrated DB for bioinformatics: a case study on analysis of functional effect of MiRNA SNPs in cancer. In: 7th International Conference on Information Technology in Bio- and Medical Informatics, ITBAM, pp. 214–222. Springer International Publishing, Porto (2016)Google Scholar
  12. 12.
    Alice A.I. Foundation: Alice. http://www.alicebot.org/
  13. 13.
    Foundation, Alice A.I.: Program AB. https://code.google.com/archive/p/program-ab/
  14. 14.
    The Eclipse Foundation: Jetty. http://www.eclipse.org/jetty/

Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Antonio Messina
    • 1
  • Agnese Augello
    • 1
  • Giovanni Pilato
    • 1
  • Riccardo Rizzo
    • 1
  1. 1.ICAR-CNRPalermoItaly

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