Skip to main content
SpringerLink
Log in

Extraction of Temporal Information from Clinical Narratives

  • Research Article
  • Published:
Journal of Healthcare Informatics Research Aims and scope Submit manuscript

Abstract

The existence of massive quantity of clinical text in electronic medical records (EMRs) has created significant demand for clinical text processing and information extraction in the field of health care and medical research. Detailed clinical observations of patients are typically recorded chronologically. Temporal information in such clinical texts consist of three elements: temporal expressions, temporal events, and temporal relations. Due to the implicit expression of temporal information, lack of writing quality, and domain-specific nature in the clinical text, extraction of temporal information is much more complex than for newswire texts. In spite of these difficulties, to extract temporal information using the annotated corpora, few research works reported rule-based, machine-learning, and hybrid methods. On the other hand, creating the annotated corpora is expensive, time-consuming, and demands significant human effort; the processing quality is inevitably affected by the small size of corpora. Motivated by this issue, in this research work, we present a novel method to effectively extract the temporal information from EMR clinical texts. The essential idea of this method is first to build a feature set appropriately for clinical expressions, followed by the development of a semi-supervised framework for temporal event extraction, and finally detection of temporal relations among events with a newly formulated hypothesis. Comparative experimental evaluation on the I2B2 data set has clearly shown improved performance of the proposed methods. Specifically, temporal event and relation extraction is possible with an F-measure 89.98 and 67.1% respectively.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Notes

  1. https://www.i2b2.org/NLP/TemporalRelations/

  2. http://alt.qcri.org/semeval2015/

  3. http://alt.qcri.org/semeval2016/

  4. https://physionet.org/mimic2/mimic2_clinical_overview.shtml

  5. https://www.i2b2.org/NLP/TemporalRelations/

  6. http://clear.colorado.edu/compsem/documents/THYME_guidelines.pdf

  7. https://github.com/HeidelTime/heideltime/

  8. https://sourceforge.net/projects/crfpp/

  9. http://mallet.cs.umass.edu/semi-sup-fst.php

  10. https://metamap.nlm.nih.gov/

  11. http://www.nactem.ac.uk/GENIA/tagger/

  12. http://www.nltk.org/api/nltk.tag.html

  13. http://www.cs.waikato.ac.nz/ml/weka/

References

  1. Aggarwal CC, Zhai C (2012) A survey of text clustering algorithms. In: Mining text data, pp 77–128. Springer

  2. Agrawal A (2009) Medication errors: prevention using information technology systems. Br J Clin Pharmacol 67(6):681–686

    Article  Google Scholar 

  3. Allen JF (1983) Maintaining knowledge about temporal intervals. Commun ACM 26(11):832–843

    Article  MATH  Google Scholar 

  4. Ambit H, Gonzalo C (2016) Clinical narrative analytics challenges. In: Proceedings Rough Sets: International Joint Conference, IJCRS 2016, Santiago de Chile, Chile, October 7–11, 2016, vol 9920. Springer, p 23

  5. Augusto JC (2005) Temporal reasoning for decision support in medicine. Artif Intell 33(1):1–24

    MathSciNet  Google Scholar 

  6. Bethard S, Derczynski L, Savova G, Savova G, Pustejovsky J, Verhagen M (2015) Semeval-2015 task 6: clinical tempeval. In: Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), pp 806–814

  7. Bethard S, Savova G, Chen WT, Derczynski L, Pustejovsky J, Verhagen M (2016) Semeval-2016 task 12: clinical tempeval. In: Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval 2016), San Diego, California, June. Association for Computational Linguistics, pp 962–972

  8. Blei DM, Ng AY, Jordan MI (2003) Latent Dirichlet allocation. J Mach Learn Res 3(Jan):993–1022

    MATH  Google Scholar 

  9. Chambers N, Wang S, Jurafsky D (2007) Classifying temporal relations between events. In: Proceedings of the 45th Annual Meeting of the ACL on Interactive Poster and Demonstration Sessions, ACL ’07, pp 173-176. Association for Computational Linguistics, Stroudsburg, PA, USA

  10. Dubois S, Kale DC, Shah N, Jung K (2017) Learning effective representations from clinical notes. arXiv:1705.07025

  11. Feldman K, Hazekamp N, Chawla NV (2016) Mining the clinical narrative: all text are not equal. In: 2016 IEEE international conference on healthcare informatics (ICHI), pp 271–280. IEEE

  12. Galescu L, Nate B (2012) A corpus of clinical narratives annotated with temporal information. In: Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, pp 715–720

  13. Grishman R, Sundheim B (1996) Message understanding conference-6: a brief history. In: COLING 1996 Volume 1: The 16th international conference on computational linguistics, vol 1

  14. Styler WF IV, Bethard S, Finan S, Palmer M, Pradhan S, de Groen PC, Erickson B, Miller T, Lin C, Savova G, Pustejovsky J (2014) Temporal annotation in the clinical domain. Trans Assoc Comput Linguist 2:143–154

    Article  Google Scholar 

  15. Jiao F, Wang S, Lee CH, Greiner R, Schuurmans D (2006) Semi-supervised conditional random fields for improved sequence segmentation and labeling. In: Proceedings of the 21st international conference on computational linguistics and the 44th annual meeting of the association for computational linguistics, pp 209–216. Association for computational linguistics

  16. Jindal P, Roth D (2013) Extraction of events and temporal expressions from clinical narratives. J Biomed Inform 46, Supplement(0):S13 – S19. https://doi.org/10.1016/j.jbi.2013.08.010. 2012 i2b2 {NLP} challenge on temporal relations in clinical data

    Article  Google Scholar 

  17. Kanungo T, Mount DM, Netanyahu NS, Piatko CD, Silverman R, Wu AY (2002) An efficient k-means clustering algorithm: analysis and implementation. IEEE Trans Pattern Anal Mach Intell 24(7):881–892

    Article  MATH  Google Scholar 

  18. Lafferty J, McCallum A, Pereira F (2001) Conditional random fields: probabilistic models for segmenting and labeling sequence data. In: Proceedings of the 18th international conference on machine learning, ICML, vol 1, pp 282–289

  19. Zhou L, Friedman C, Parsons S, Hripcsak G (2005) System architecture for temporal information extraction, representation and reasoning in clinical narrative reports. Am Med Inform Assoc 2005:869

    Google Scholar 

  20. Liu Y, LePendu P, Iyer S, Shah NH (2012) Using temporal patterns in medical records to discern adverse drug events from indications. AMIA Summits Transl Sci Proc 2012:47–56

    Google Scholar 

  21. Long Y, Li Z, Wang X, Li C (2017) XJNLP at SemEval-2017 Task 12: clinical temporal information extraction with a hybrid model. In: Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp 1014–1018

  22. Mani I (2004) Recent developments in temporal information extraction. In: Proceedings of the international conference on recent advances in natural language processing (RANLP’03), pp 45–60

  23. Martinho R (2015) Text mining applied to electronic medical records. Int J E-Health Med Commun 6(3):1–18

    Article  Google Scholar 

  24. Miller TA, Bethard S, Dligach D, Lin C, Savova GK (2015) Extracting time expressions from clinical text, pp 81–91

  25. Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H (2011) A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc 18(5):601–606

    Article  Google Scholar 

  26. Moharasan G, Ho TB (2016) A semi-supervised approach for temporal information extraction from clinical text. In: 2016 IEEE RIVF international conference on computing & communication technologies, research, innovation, and vision for the future (RIVF), pp 7–12. IEEE

  27. Moharasan G, Ho TB (2017) Extraction of temporal events from clinical text using semi-supervised conditional random fields. In: International conference on data mining and big data, pp 409–421. Springer

  28. Pustejovsky J, Hanks P, Sauri R, See A, Gaizauskas R, Setzer A, Radev D, Sundheim B, Day D, Ferro L et al (2003) The timebank corpus. In: Corpus linguistics, vol 2003, p 40

  29. Pustejovsky J, Lee K, Bunt H, Romary L (2010) Iso-timeml: an international standard for semantic annotation. LREC 2010

  30. Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Setzer A, Roberts I (2008) Semantic annotation of clinical text: the CLEF corpus. In: Proceedings of the LREC 2008 workshop on building and evaluating resources for biomedical text mining, pp 19–26

  31. Sohn S, Wagholikar K, Li D, Jonnalagaddaa S, Tao C, Elayavilli RK, Liu H (2013) Comprehensive temporal information detection from clinical text: medical events, time, and tlink identification. JAMIA 20(5):836–842

    Google Scholar 

  32. Sun W, Rumshisky A, Uzuner O (2013) Annotating temporal information in clinical narratives. J Biomed Inform 46:s5–s12

    Article  Google Scholar 

  33. Sun W, Rumshisky A, Uzuner O (2013) Evaluating temporal relations in clinical text: 2012 i2b2 challenge. J Am Med Inform Assoc 20(5):806–813

    Article  Google Scholar 

  34. Sun W, Rumshisky A, Uzuner O (2013) Temporal reasoning over clinical text: the state of the art. J Am Med Inform Assoc 20(5):814–819

    Article  Google Scholar 

  35. Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H (2013) A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc 20(5):828–835

    Article  Google Scholar 

  36. Tao C, Filannino M, Uzuner Ö (2017) Prescription extraction using CRFs and word embeddings. Journal of biomedical informatics 72:60–66

    Article  Google Scholar 

  37. Trivedi G, Pham P, Chapman W, Hwa R, Wiebe J, Hochheiser H (2017) An interactive tool for natural language processing on clinical text. arXiv:1707.01890

  38. UzZaman N, Llorens H, Allen J, Derczynski L, Verhagen M, Pustejovsky J (2012) Tempeval-3: Evaluating events, time expressions, and temporal relations. arXiv:1206.5333

  39. Verhagen M, Gaizauskas R, Schilder F, Hepple M, Moszkowicz J, Pustejovsky J (2009) The tempeval challenge: identifying temporal relations in text. Lang Resour Eval 43(2):161–179

    Article  Google Scholar 

  40. Verhagen M, Sauri R, Caselli T, Pustejovsky J (2010) SemEval-2010 task 13: TempEval-2. In: Proceedings of the 5th international workshop on semantic evaluation, pp 57–62. Association for Computational Linguistics

  41. Vilain MB, Kautz HA (1986) Constraint propagation algorithms for temporal reasoning. In: Aaai, vol 86, pp 377–382

  42. Wang CC, Chien MN, Huang CH, Liu L (2007) A rule-based disease diagnostic system using a temporal relationship model. In: 4th international conference on fuzzy systems and knowledge discovery, 2007. FSKD 2007. vol 4, pp 109–115. IEEE

  43. Wang Y, Rastegar-Mojarad M, Elayavilli RK, Liu S, Liu H (2016) An ensemble model of clinical information extraction and information retrieval for clinical decision support. In: TREC

  44. Wang Y, Wang L, Rastegar-Mojarad M, Moon S, Shen F, Afzal N, Liu S, Zeng Y, Mehrabi S, Sohn S et al (2017) Clinical information extraction applications: a literature review. Journal of biomedical informatics

  45. Wong KF, Xia Y, Li W, Yuan C (2005) An overview of temporal information extraction. Int J Comput Process Orient Lang 18(02):137–152

    Article  Google Scholar 

  46. Lin YK, Chen H, Brown RA (2013) Medtime: a temporal information extraction system for clinical narratives. J Biomed Inform 46:s20–s28

    Article  Google Scholar 

  47. Chang YC, Dai HJ, Wu JC, Chen JM, Tsai RT, Hsu WL (2013) Tempting system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries. J Biomed Inform 46:s54–s62

    Article  Google Scholar 

  48. Zhou L, Hripcsak G (2007) Temporal reasoning with medical data-a review with emphasis on medical natural language processing. J Biomed Inform 40(2):183–202

    Article  Google Scholar 

  49. Zhu X (2005) Semi-supervised learning literature survey. World 10:10

    Google Scholar 

  50. Zhu X, Cherry C, Kiritchenko S, Martin J, De Bruijn B (2013) Detecting concept relations in clinical text: insights from a state-of-the-art model. J Biomed Inform 46(2):275–285

    Article  Google Scholar 

Download references

Acknowledgments

We are grateful to MAYO CLINIC and Informatics for Integrating Biology and the Bedside (I2B2) organizers for providing access to annotated I2B2 temporal relations corpus.

Funding

This work is partially supported by Japan Ministry of Education, Culture, Sports, Science and Technology scholarship and the Vietnam National University at Ho Chi Minh City under the grant no. B2015-42-02.

Author information

Authors and Affiliations

  1. Japan Advanced Institute of Science and Technology, Nomi, Japan

    Gandhimathi Moharasan & Tu-Bao Ho

  2. John Von Neumann Institute, VNU-HCM, Ho Chi Minh City, Vietnam

    Tu-Bao Ho

Authors
  1. Gandhimathi Moharasan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tu-Bao Ho
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gandhimathi Moharasan.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This article is part of the Topical Collection on Special Issue on Healthcare Knowledge Discovery and Management

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moharasan, G., Ho, TB. Extraction of Temporal Information from Clinical Narratives. J Healthc Inform Res 3, 220–244 (2019). https://doi.org/10.1007/s41666-019-00049-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s41666-019-00049-0

Keywords

Search

Navigation