Abstract
This paper outlines a system, OntoScape, serving to accomplish complex inference tasks on knowledge bases and bio-models derived from life-science text corpora. The system applies so-called natural logic, a form of logic which is readable for humans. This logic affords ontological representations of complex terms appearing in the text sources. Along with logical propositions, the system applies a semantic graph representation facilitating calculation of bio-pathways. More generally, the system affords means of query answering appealing to general and domain specific inference rules.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Schultz, S., Hahn, U.: Towards the ontological foundations of symbolic biological theories. Artif. Intell. Med. 39, 237–250 (2007)
Bittner, T., Donelly, M.: Logical properties of foundational relations in bio-ontologies. Artif. Intell. Med. 39, 197–216 (2007)
Andreasen, T., Bulskov, H., Fischer Nilsson, J., Jensen, P.A.: On the relationship between a computational natural logic and natural language. In: The 8th International Conference on Agents and Artificial Intelligence, ICAART, pp. 335–342 (2016)
Andreasen, T., Bulskov, H., Fischer Nilsson, J., Anker Jensen, P., Lassen, T.: Conceptual pathway querying of natural logic knowledge bases from text bases. In: Larsen, H.L., Martin-Bautista, M.J., Vila, M.A., Andreasen, T., Christiansen, H. (eds.) FQAS 2013. LNCS, vol. 8132, pp. 1–12. Springer, Heidelberg (2013). doi:10.1007/978-3-642-40769-7_1
Andreasen, T., Bulskov, H., Fischer Nilsson, J., Jensen, P.A.: A system for conceptual pathway finding and deductive querying. In: Andreasen, T., et al. (eds.) Flexible Query Answering Systems, vol. 400, pp. 461–472. Springer, Cham (2015). doi:10.1007/978-3-319-26154-6_35
Fischer Nilsson, J.: Diagrammatic reasoning with classes and relationships. In: Moktefi, A., Shin, S.-J. (eds.) Visual Reasoning with Diagrams. Studies in Universal Logic. Birkhäuser, Springer, Basel (2013)
van Benthem, J.: Essays in Logical Semantics. Studies in Linguistics and Philosophy, vol. 29. D. Reidel Publishing Company, Dordrecht (1986)
Smith, B., Rosse, C.: The role of foundational relations in the aligment of biomedical ontologies. In: Fieschi, M., et al. (eds.) MEDINFO 2004 (2004)
Vechina, A., et al.: Representation of semantic networks of biomedical terms. In: Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain (2013)
Miljkovic, D., et al.: Incremental revision of biological networks from texts. In: Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain (2013)
Quesada-Martinéz, M., et al.: Analysis and classification of bio-ontologies by the structure of their labels. In: Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain (2013)
Endocrine Gland (2015). Wikipedia. http://en.wikipedia.org/wiki/Endocrine_gland. Accessed 6 Mar 2016
Li, C., Liakata, M., Rebholz-Schuhmann, D.: Biological network extraction from scientific literature: state of the art and challenges. Briefings Bioinform. 15(5), 856–877 (2013)
Kaewphan, S., Kreula, S., Van Landeghem, S., Van de Peer, Y., Jones, P.R., Ginter, F.: Integrating large-scale text mining and co-expression networks: targeting NADP(H) metabolism in E. coli with event extraction. In: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), pp. 8–15 (2012)
Hakala, K., Van Landeghem, S., Kaewphan, S., Salakoski, T., Van de Peer, Y., Ginter, F.: CyEVEX: literature-scale network integration and visualization through Cytoscape. In: Proceedings of SMBM 2012, pp. 91–96, Zurich, Switzerland (2012)
Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D.B., Pyysalo, S., Ananiadou, S.: A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinformatics 29(13), i44–i52 (2013)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Andreasen, T., Bulskov, H., Jensen, P.A., Nilsson, J.F. (2017). Pathway Computation in Models Derived from Bio-Science Text Sources. In: Kryszkiewicz, M., Appice, A., Ślęzak, D., Rybinski, H., Skowron, A., Raś, Z. (eds) Foundations of Intelligent Systems. ISMIS 2017. Lecture Notes in Computer Science(), vol 10352. Springer, Cham. https://doi.org/10.1007/978-3-319-60438-1_42
Download citation
DOI: https://doi.org/10.1007/978-3-319-60438-1_42
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-60437-4
Online ISBN: 978-3-319-60438-1
eBook Packages: Computer ScienceComputer Science (R0)