Abstract
Rule-based formalization of eligibility criteria in clinical trials have distinguished features such as declaration, easy maintenance, reusability, and expressiveness. In this paper, we present several knowledge services which can be provided by the rule-based formalization of eligibility criteria. The rule-based formalization can be generated automatically by using the logic programming Prolog with the support of NLP tools for the semantic annotation and relation extraction with medical ontologies/terminologies such as UMLS and SNOMED CT. We show how those automatically generated rule-based formalization for eligibility criteria can be used for the patient recruitment service in SemanticCT, a semantically-enabled system for clinical trials.
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References
Ait-Mokhtar, S., Bruijn, B.D., Hagege, C., Rupi, P.: Initial prototype for relation identification between concepts, D3.2. Technical report, EURECA Project (2013)
Ait-Mokhtar, S., Bruijn, B.D., Hagege, C., Rupi, P.: Intermediary-stage ie components, D3.5. Technical report, EURECA Project (2014)
Aït-Mokhtar, S., Chanod, J.-P., Roux, C.: Robustness beyond shallowness: incremental deep parsing. Nat. Lang. Eng. 8(2), 121–144 (2002)
Aronson, A.R., Lang, F.: An overview of metamap: historical perspective and recent advances. J. Am. Med. Inf. Assoc.: JAMIA 17(3), 229–236 (2010)
Bucur, A., ten Teije, A., van Harmelen, F., Tagni, G., Kondylakis, H., van Leeuwen, J., Schepper, K.D., Huang, Z.: Formalization of eligibility conditions of CT and a patient recruitment method, D6.1. Technical report, EURECA Project (2012)
Fensel, D., van Harmelen, F., Andersson, B., Brennan, P., Cunningham, H., Della Valle, E., Fischer, F., Huang, Z., Kiryakov, A., Lee, T., School, L., Tresp, V., Wesner, S., Witbrock, M., Zhong, N.: Towards LarKC: a platform for web-scale reasoning. In: Proceedings of the IEEE International Conference on Semantic Computing (ICSC). IEEE Computer Society Press, CA (2008)
Huang, Z., Teije, A., Harmelen, F.: Rule-based formalization of eligibility criteria for clinical trials. In: Peek, N., MarÃn Morales, R., Peleg, M. (eds.) AIME 2013. LNCS (LNAI), vol. 7885, pp. 38–47. Springer, Heidelberg (2013). doi:10.1007/978-3-642-38326-7_7
Huang, Z., ten Teije, A., van Harmelen, F.: SemanticCT: a semantically-enabled system for clinical trials. In: Riaño, D., Lenz, R., Miksch, S., Peleg, M., Reichert, M., ten Teije, A. (eds.) KR4HC/ProHealth -2013. LNCS (LNAI), vol. 8268, pp. 11–25. Springer, Heidelberg (2013). doi:10.1007/978-3-319-03916-9_2
Huang, Z., van Harmelen, F., ten Teije, A., Dekker, A.: Feasibility estimation for clinical trials. In: Proceedings of the 7th International Conference on Health Informatics (HEALTHINF 2014), Angers, Loire Valley, France, 3–6 March 2014
Huang, Z., van Harmelen, F., ten Teije, A., Dentler, K.: Knowledge-based patient data generation. In: Riaño, D., Lenz, R., Miksch, S., Peleg, M., Reichert, M., ten Teije, A. (eds.) KR4HC/ProHealth 2013. LNCS (LNAI), vol. 8268, pp. 83–96. Springer, Heidelberg (2013). doi:10.1007/978-3-319-03916-9_7
Khiari, A.: Identification of variants of compound terms, master thesis. Technical report, Universite Paul Sabatier, Toulouse (2015)
Milian, K., Teije, A.: Towards automatic patient eligibility assessment: from free-text criteria to queries. In: Peek, N., MarÃn Morales, R., Peleg, M. (eds.) AIME 2013. LNCS (LNAI), vol. 7885, pp. 78–83. Springer, Heidelberg (2013). doi:10.1007/978-3-642-38326-7_12
Pyysalo, S., Ananiadou, S.: Anatomical entity mention recognition at literature scale. Bioinformatics 30(6), 868–875 (2014)
Spackman, K.: Managing clinical terminology hierarchies using algorithmic calculation of subsumption: Experience with snomed-rt. J. Am. Med. Inf. Assoc. (2000)
Tu, S., Peleg, M., Carini, S., Bobak, M., Ross, J., Rubin, D., Sim, I.: A practical method for transforming free-text eligibility criteria into computable criteria. JBI 44(2), 239–250 (2011)
Wielemaker, J., Huang, Z., van der Meij, L.: SWI-Prolog and the web. J. Theory Pract. Logic Program. 8(3), 363–392 (2008)
Wielemaker, J., Schrijvers, T., Triska, M., Lager, T.: SWI-Prolog. J. Theory Pract. Logic Program. 12(1–2), 67–96 (2012)
Witbrock, M., Fortuna, B., Bradesko, L., Kerrigan, M., Bishop, B., van Harmelen, F., ten Teije, A., Oren, E., Momtchev, V., Tenschert, A., Cheptsov, A., Roller, S., Gallizo, G.: D5.3.1 - requirements analysis and report on lessons learned during prototyping. Larkc project deliverable, June 2009
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This work is partially supported by the Dutch national project COMMIT/Data2Semantics.
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Huang, Z., Hu, Q., ten Teije, A., van Harmelen, F., Ait-Mokhtar, S. (2016). Knowledge Services Using Rule-Based Formalization for Eligibility Criteria of Clinical Trials. In: Yin, X., Geller, J., Li, Y., Zhou, R., Wang, H., Zhang, Y. (eds) Health Information Science. HIS 2016. Lecture Notes in Computer Science(), vol 10038. Springer, Cham. https://doi.org/10.1007/978-3-319-48335-1_6
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