Skip to main content

Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information

  • Conference paper
  • First Online:
Biomedical Engineering Systems and Technologies (BIOSTEC 2020)

Abstract

Personalised treatment is usually needed for hospitalised patients afflicted by secondary illnesses that demand daily medication. Even though clinical guidelines were designed to consider those circumstances exist, current decision-support features fail to assimilate detailed relevant patient information. This creates opportunities for the development of systems capable of performing a real-time evaluation of such data against existing knowledge and providing recommendations during clinical treatments. Herein, we describe a proposal for a new feature to be integrated with electronic health record (EHR) systems which can enrich the health treatment process through the automatic extraction of information from patient medical notes and the aggregation of this novel information in clinical protocols. The purpose of this work is to exploit the historical component of the patient trajectory to improve the performance of clinical decision support systems.

J. F. Silva—Contributed equally with the first author to this work.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Almeida, J.R., Guimarães, J., Oliveira, J.L.: Simplifying the digitization of clinical protocols for diabetes management. In: 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), pp. 176–181. IEEE (2018)

    Google Scholar 

  2. Almeida, J.R., Oliveira, J.L.: GenericCDSS-a generic clinical decision support system. In: 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), pp. 186–191. IEEE (2019)

    Google Scholar 

  3. Almeida, J.R., Matos, S.: Rule-based extraction of family history information from clinical notes. In: Proceedings of the 35th Annual ACM Symposium on Applied Computing, SAC 2020, pp. 670–675. Association for Computing Machinery, New York (2020). https://doi.org/10.1145/3341105.3374000

  4. Almeida, J.R., Silva, J.F., Sierra, A.P., Matos, S., Oliveira, J.L.: Enhancing decision-making systems with relevant patient information by leveraging clinical notes. In: Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies, vol. 5 HEALTHINF: HEALTHINF, pp. 254–262. INSTICC, SciTePress (2020)

    Google Scholar 

  5. Antunes, R., Silva, J.F., Pereira, A., Matos, S.: Rule-based and machine learning hybrid system for patient cohort selection. In: Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies, vol. 2: HEALTHINF, pp. 59–67. INSTICC, SciTePress (2019). https://doi.org/10.5220/0007349300590067

  6. Boxwala, A.A., et al.: GLIF3: a representation format for sharable computer-interpretable clinical practice guidelines. J. Biomed. Inform. 37(3), 147–161 (2004)

    Article  Google Scholar 

  7. Bright, T.J., et al.: Effect of clinical decision-support systems: a systematic review. Ann. Intern. Med. 157(1), 29–43 (2012)

    Article  Google Scholar 

  8. Cohen, R., Elhadad, M., Elhadad, N.: Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies. BMC Bioinform. 14(10), 1–15 (2013). https://doi.org/10.1186/1471-2105-14-10

    Article  Google Scholar 

  9. Costa, C.M.A.: Concepção, desenvolvimento e avaliação de um modelo integrado de acesso a registos clínicos electrónicos. Ph.D. thesis, University of Aveiro (2004). http://hdl.handle.net/10773/18802

  10. HMS: 2018 n2c2 - Track 1: Cohort Selection for Clinical Trials (2018). https://portal.dbmi.hms.harvard.edu/projects/n2c2-t1/

  11. HMS: 2019 n2c2 Shared-Task and Workshop, Track2: n2c2/OHNLP Track on Family History Extraction (2019). https://n2c2.dbmi.hms.harvard.edu/track2

  12. HMS: 2019 n2c2 Shared-Task and Workshop, Track3: n2c2/UMass Track on Clinical Concept Normalization (2019). https://n2c2.dbmi.hms.harvard.edu/track3

  13. Hripcsak, G., Albers, D.J.: Next-generation phenotyping of electronic health records. J. Am. Med. Inform. Assoc. 20(1), 117–121 (2012). https://doi.org/10.1136/amiajnl-2012-001145

    Article  Google Scholar 

  14. Inzucchi, S.E.: Management of hyperglycemia in the hospital setting. N. Engl. J. Med. 355(18), 1903–1911 (2006)

    Article  Google Scholar 

  15. Jensen, K., et al.: Analysis of free text in electronic health records for identification of cancer patient trajectories. Sci. Rep. 7(46226), 1–12 (2017). https://doi.org/10.1038/srep46226

    Article  Google Scholar 

  16. Katehakis, D.G., Tsiknakis, M.: Electronic health record. In: Wiley Encyclopedia of Biomedical Engineering. Wiley (2006). https://doi.org/10.1002/9780471740360.ebs1440

  17. Kim, Y., Rajan, K.B., Sims, S.A., Wroblewski, K.E., Reutrakul, S.: Impact of glycemic variability and hypoglycemia on adverse hospital outcomes in non-critically ill patients. Diab. Res. Clin. Pract. 103(3), 437–443 (2014)

    Article  Google Scholar 

  18. Manning, C.D., Surdeanu, M., Bauer, J., Finkel, J., Bethard, S.J., McClosky, D.: The Stanford CoreNLP natural language processing toolkit. In: Association for Computational Linguistics (ACL) System Demonstrations, pp. 55–60 (2014). http://www.aclweb.org/anthology/P/P14/P14-5010

  19. Matos, S.: Configurable web-services for biomedical document annotation. J. Cheminform. 10(1), 68 (2018)

    Article  Google Scholar 

  20. Miotto, R., Wang, F., Wang, S., Jiang, X., Dudley, J.T.: Deep learning for healthcare: review, opportunities and challenges. Brief. Bioinform. (2017). https://doi.org/10.1093/bib/bbx044

    Article  Google Scholar 

  21. NCCIH: Clinical Practice Guidelines (2017). https://nccih.nih.gov/health/providers/clinicalpractice.htm

  22. Neinstein, A., MacMaster, H.W., Sullivan, M.M., Rushakoff, R.: A detailed description of the implementation of inpatient insulin orders with a commercial electronic health record system. J. Diab. Sci. Technol. 8(4), 641–651 (2014)

    Article  Google Scholar 

  23. Nelson, S.J., Zeng, K., Kilbourne, J., Powell, T., Moore, R.: Normalized names for clinical drugs: RxNorm at 6 years. J. Am. Med. Inform. Assoc. 18(4), 441 (2011). https://doi.org/10.1136/amiajnl-2011-000116

    Article  Google Scholar 

  24. Neustein, A., Imambi, S.S., Rodrigues, M., Teixeira, A., Ferreira, L.: Application of text mining to biomedical knowledge extraction: analyzing clinical narratives and medical literature. In: Text Mining of Web-based Medical Content, pp. 3–32. De Gruyter (2014). https://doi.org/10.1515/9781614513902.3

  25. O’Connor, P.J., et al.: Impact of electronic health record clinical decision support on diabetes care: a randomized trial. Ann. Fam. Med. 9(1), 12–21 (2011). https://doi.org/10.1370/afm.1196

    Article  Google Scholar 

  26. Pivovarov, R., Elhadad, N.: Automated methods for the summarization of electronic health records. J. Am. Med. Inform. Assoc. 22(5), 938–947 (2015). https://doi.org/10.1093/jamia/ocv032

    Article  Google Scholar 

  27. Sheikhalishahi, S., Miotto, R., Dudley, J.T., Lavelli, A., Rinaldi, F., Osmani, V.: Natural language processing of clinical notes on chronic diseases: systematic review. JMIR Med. Inform. 7(2), e12239 (2019). https://doi.org/10.2196/12239. http://medinform.jmir.org/2019/2/e12239/

  28. Shetty, S., Inzucchi, S., Goldberg, P., Cooper, D., Siegel, M., Honiden, S.: Adapting to the new consensus guidelines for managing hyperglycemia during critical illness: the updated Yale insulin infusion protocol. Endocr. Pract. 18(3), 363–370 (2011)

    Article  Google Scholar 

  29. Silva, J.F., Antunes, R., Almeida, J.R., Matos, S.: Clinical concept normalization on medical records using word embeddings and heuristics. In: 30th Medical Informatics Europe Conference, MIE (2020)

    Google Scholar 

  30. Singh, H., Giardina, T.D., Meyer, A.N.D., Forjuoh, S.N., Reis, M.D., Thomas, E.J.: Types and origins of diagnostic errors in primary care settings. JAMA Intern. Med. 173(6), 418–425 (2013). https://doi.org/10.1001/jamainternmed.2013.2777

    Article  Google Scholar 

  31. Stearns, M.Q., Price, C., Spackman, K.A., Wang, A.Y.: SNOMED clinical terms: overview of the development process and project status. In: Proceedings of the AMIA Symposium, pp. 662–666. American Medical Informatics Association, Washington (2001). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2243297/

  32. Stewart, W.F., Shah, N.R., Selna, M.J., Paulus, R.A., Walker, J.M.: Bridging the inferential gap: the electronic health record and clinical evidence. Health Affairs 26(Supplement 1), w181–w191 (2007). https://doi.org/10.1377/hlthaff.26.2.w181

  33. Stubbs, A., Kotfila, C., Xu, H., Uzuner, Ö.: Identifying risk factors for heart disease over time: overview of 2014 i2b2/UTHealth shared task track 2. J. Biomed. Inform. 58, S67–S77 (2015)

    Article  Google Scholar 

  34. Umpierrez, G.E., et al.: Safety and efficacy of sitagliptin therapy for the inpatient management of general medicine and surgery patients with type 2 diabetes: a pilot, randomized, controlled study. Diab. Care 36(11), 3430–3435 (2013)

    Article  Google Scholar 

  35. Umpierrez, G.E., et al.: Management of hyperglycemia in hospitalized patients in non-critical care setting: an endocrine society clinical practice guideline. J. Clin. Endocrinol. Metab. 97(1), 16–38 (2012)

    Article  Google Scholar 

  36. Wexler, D.J., Shrader, P., Burns, S.M., Cagliero, E.: Effectiveness of a computerized insulin order template in general medical inpatients with type 2 diabetes: a cluster randomized trial. Diab. Care 33(10), 2181–2183 (2010)

    Article  Google Scholar 

  37. WHO: World Health Organization: International classification of diseases, 11th Revision (ICD-11) (2018). https://www.who.int/classifications/icd/en/

Download references

Acknowledgements

This work has received support from the EU/EFPIA Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 806968 and from the NETDIAMOND project (POCI-01-0145-FEDER-016385), co-funded by Centro 2020 program, Portugal 2020, European Union. João Figueira Silva and João Rafael Almeida are funded by the FCT - Foundation for Science and Technology (national funds) under the grants PD/BD/142878/2018 and SFRH/BD/147837/2019 respectively.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to João Rafael Almeida .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Almeida, J.R., Silva, J.F., Sierra, A.P., Matos, S., Oliveira, J.L. (2021). Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. In: Ye, X., et al. Biomedical Engineering Systems and Technologies. BIOSTEC 2020. Communications in Computer and Information Science, vol 1400. Springer, Cham. https://doi.org/10.1007/978-3-030-72379-8_26

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-72379-8_26

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-72378-1

  • Online ISBN: 978-3-030-72379-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics