Advertisement

Example Based Programming and Ontology Building: A Bioinformatic Application

  • Quentin Riché-PiotaixEmail author
  • Patrick Girard
  • Frédéric Bilan
  • Ladjel Bellatreche
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 850)

Abstract

To find ways to facilitate the querying process of heterogeneous databases reveals a critical research avenue, especially in biology. Making use of ontologies is considered one of the best solutions, which makes the activity of ontology design critical for biologists. However, such design process is not easily attainable by non-experts, issue sublimated by the constant evolution of the domain taxonomies [1]. Moreover, designing ontologies currently requires some expert knowledge of the domain as well as skills in database and ontology modelling. This fact was corroborated by our pilot study involving geneticists from the Poitiers hospital. The specialists did not possess any prior knowledge of conceptual data models. Nevertheless, they were able to build their own mental model of the situation that could later be correlated to the actual database models.

Compared to previous End-User Programming approaches, this experiment shows that End-User Programming techniques permit to build and use conceptual models without any need for specific training. In this poster, we describe the pilot study we conducted using geneticists during the dedicated ontologies design process that allows querying public databases. Several specific constraints were identified, along with their proposed solutions. A complete example of ontology design, built from the genetic field, is then described.

Keywords

Ontology Database Human-computer interaction Genetic Bioinformatic 

References

  1. 1.
    Petasis, G., Karkaletsis, V., Paliouras, G., Krithara, A., Zavitsanos, E.: Ontology population and enrichment: state of the art. In: Paliouras, G., Spyropoulos, C.D., Tsatsaronis, G. (eds.) Knowledge-Driven Multimedia Information Extraction and Ontology Evolution. LNCS (LNAI), vol. 6050, pp. 134–166. Springer, Heidelberg (2011).  https://doi.org/10.1007/978-3-642-20795-2_6CrossRefGoogle Scholar
  2. 2.
    Letondal, C.: Interaction and programming. Ph.D. thesis, Université Paris Sud - Paris XI (2001)Google Scholar
  3. 3.
    Cypher, A., Halbert, D.C.: Watch What I Do: Programming by Demonstration. MIT press, Cambridge (1993)Google Scholar
  4. 4.
    Lieberman, H.: Your Wish is My Command: Programming by Example. Morgan Kaufmann, Burlington (2001)Google Scholar
  5. 5.
    Girard, P.: Bringing programming by demonstration to cad users. In: Your Wish is My Command, pp. 135–VII. Elsevier (2001)Google Scholar
  6. 6.
    Goubali, O., Girard, P., Guittet, L., Bignon, A., Kesraoui, D., Berruet, P., Bouillon, J.-F.: Designing functional specifications for complex systems. In: Kurosu, M. (ed.) HCI 2016. LNCS, vol. 9731, pp. 166–177. Springer, Cham (2016).  https://doi.org/10.1007/978-3-319-39510-4_16CrossRefGoogle Scholar
  7. 7.
    Lefrançois, M., Zimmermann, A., Bakerally, N.: Génération de RDF à partir de sources de données aux formats hétérogènes (2017)Google Scholar
  8. 8.
    Kim, S., Alani, H., Hall, W., Lewis, P., Millard, D., Shadbolt, N., Weal, M.: Artequakt: generating tailored biographies from automatically annotated fragments from the web (2002)Google Scholar
  9. 9.
    O’Connor, M.J., Halaschek-Wiener, C., Musen, M.A.: Mapping master: a flexible approach for mapping spreadsheets to OWL. In: Patel-Schneider, P.F., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J.Z., Horrocks, I., Glimm, B. (eds.) ISWC 2010. LNCS, vol. 6497, pp. 194–208. Springer, Heidelberg (2010).  https://doi.org/10.1007/978-3-642-17749-1_13CrossRefGoogle Scholar
  10. 10.
    Brewster, C., Iria, J., Zhang, Z., Ciravegna, F., Guthrie, L., Wilks, Y.: Dynamic iterative ontology learning. In: 6th International Conference on Recent Advances in Natural Language Processing (2007)Google Scholar
  11. 11.
    Dimou, A., Sande, M.V., Colpaert, P., Mannens, E., Van De Walle, R.: Extending R2RML to a source-independent mapping language for RDF. In: Proceedings of the 2013th International Conference on Posters & #38; Demonstrations Track, Aachen, Germany, ISWC-PD 2013, vol. 1035, pp. 237–240. CEUR-WS.org (2013)Google Scholar
  12. 12.
    Drumond, L., Girardi, R.: A survey of ontology learning procedures. In: de Freitas, F.L.G., Stuckenschmidt, H., Pinto, H.S., Malucelli, A., Corcho, O. (eds.) CEUR Workshop Proceedings of WONTO, vol. 427. CEUR-WS.org (2008)Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Quentin Riché-Piotaix
    • 1
    • 2
    • 3
    Email author
  • Patrick Girard
    • 1
    • 3
  • Frédéric Bilan
    • 1
    • 2
  • Ladjel Bellatreche
    • 3
  1. 1.Université de PoitiersPoitiersFrance
  2. 2.CHU de PoitiersPoitiersFrance
  3. 3.LIAS, ISAE-ENSMAPoitiersFrance

Personalised recommendations