Konferensartikel

Initial Experiments of Medication Event Extraction Using Frame Semantics

Dimitrios Kokkinakis
Department of Swedish Language, University of Gothenburg, Gothenburg, Sweden

Ladda ner artikel

Ingår i: Scandinavian Conference on Health Informatics 2012; October 2-3; Linköping; Sverige

Linköping Electronic Conference Proceedings 70:7, s. 41-47

Visa mer +

Publicerad: 2012-09-28

ISBN: 978-91-7519-758-6

ISSN: 1650-3686 (tryckt), 1650-3740 (online)

Abstract

Semantic annotation of text corpora for mining complex relations and events has gained a considerable growing attention in the medical domain. The goal of this paper is to present a snapshot of ongoing work that aims to develop and apply an appropriate infrastructure for automatic event labelling and extraction in the Swedish medical domain. Annotated text samples; appropriate lexical resources (e.g. term lists and the Swedish Frame-Net++) and hybrid techniques are currently developed in order to alleviate some of the difficulties of the task. As a case study this paper presents a pilot approach based on the application of the theory of frame semantics to automatically identify and extract detailed medication information from medical texts. Medication information is often written in narrative form (e.g. in clinical records) and is therefore difficult to be acquired and used in computerized systems (e.g. decision support). Currently our approach uses a combination of generic entity and terminology taggers; specifically designed medical frames and various frame-related patterns. Future work intends to improve and enhance current results by using more annotated samples; more medically-relevant frames and combination of supervised learning techniques with the regular expression patterns.

Nyckelord

Inga nyckelord är tillgängliga

Referenser

[1] Ananiadou S; Pyysalo S; Tsujii J; Kell DB. Event extraction for systems biology by text mining the literature. Trends Biotechnol. 2010 Jul;28(7):381-90.

[2] Miwa M; Thompson P; McNaught J; Kell DB; and Ananiadou S. Extracting semantically enriched events from biomedical literature. BMC Bioinformatics 2012; 13:108.

[3] Johansson R; Friberg Heppin K; and Dimitrios Kokkinakis. Semantic Role Labeling with the Swedish Frame- Net. Proceedings of the 8th International Conf on Language Resources and Evaluation (LREC’12); 2012; pp. 3697–3700. Istanbul; Turkey.

[4] Patrick J; Li M. High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge. J Am Med Inf Assoc 2010; 17:524e527.

[5] Deléger L; Grouin C; and Zweigenbaum P. Extracting medical information from narrative patient records: the case of medication-related information. J Am Med Inf Assoc 2010; 17:555e558.

[6] Doan S; Bastarache L; Klimkowski S; Denny JC; and Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. J Am Med Inf Assoc 2010; 17:528e531.

[7] Hamon T; and Grabar N. Linguistic approach for identification of medication names and related information in clinical narratives. J Am Med Inf Assoc 2010; 17:549e554.

[8] Halgrim JR; Xia F; Solti I; Cadag E; and Uzuner Ö. A cascade of classifiers for extracting medication information from discharge summaries. J of Biomed Sem 2011; 2(Suppl 3):S2

[9] Gold S; Elhadad N; Zhu X; Cimino JJ; and Hripcsak G. Extracting Structured Medication Event Information from Discharge Summaries. AMIA Annu Symp Proc. 2008; 237–241.

[10] Fillmore CJ; Johnson CR; and Petruck MRL. Background to FrameNet. Journal of Lexicography; 2003; 16(3). <http://framenet.icsi.berkeley.edu>.

[11] Dolbey A; Ellsworth M; and Scheffczyk J. BioFrameNet: A Domain-specific FrameNet Extension with Links to Biomedical Ontologies. KR-MED: "Biomedical Ontology in Action". 2006; Baltimore; Maryland; USA.

[12] Kokkinakis D. A Semantically Annotated Swedish Medical Corpus. Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC). 2008. Marrakech; Morocco.

[13] Kokkinakis D. Reducing the Effect of Name Explosion. Proceedings of the LREC Workshop: Beyond Named Entity Recognition; Semantic labelling for NLP tasks. Fourth Language Resources and Evaluation Conference (LREC). Pp. 1-6. 2004. Lissabon; Portugal.

[14] Stenetorp P.; Pyysalo S.; Topic G.; Ohta T.; Ananiadou S. and Tsujii J. BRAT: a Web-based Tool for NLP-Assisted Text Annotation. Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics. 2012. Avignon; France.

[15] Meystre S; Savova G; Kipper-Schuler Karin C; and Hurdle JE. Extracting Information from Textual Documents in the Electronic Health Record: A Review of Recent Research. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008; 47 Suppl 1: 128-144.

[16] Björne J; Ginter F; Pyysalo S; Tsujii J; and Salakoski T. Complex event extraction at PubMed scale. BioInformatics Vol. 26 ISMB 2010; pages i382–i390

Citeringar i Crossref