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Caufield JH, Zhou Y, Garlid AO, et al. A reference set of curated biomedical data and metadata from clinical case reports. Sci Data. 2018;5:180258doi: 10.1038/sdata.2018.258.
Caufield, J. H., Zhou, Y., Garlid, A. O., Setty, S. P., Liem, D. A., Cao, Q., Lee, J. M., Murali, S., Spendlove, S., Wang, W., Zhang, L., Sun, Y., Bui, A., Hermjakob, H., Watson, K. E., & Ping, P. (2018). A reference set of curated biomedical data and metadata from clinical case reports. Scientific data, 5180258. https://doi.org/10.1038/sdata.2018.258
Caufield, J Harry, et al. "A reference set of curated biomedical data and metadata from clinical case reports." Scientific data vol. 5 (2018): 180258. doi: https://doi.org/10.1038/sdata.2018.258
Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P. A reference set of curated biomedical data and metadata from clinical case reports. Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258. PMID: 30457569; PMCID: PMC6244181.
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Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258.

A reference set of curated biomedical data and metadata from clinical case reports.

Scientific data

J Harry Caufield, Yijiang Zhou, Anders O Garlid, Shaun P Setty, David A Liem, Quan Cao, Jessica M Lee, Sanjana Murali, Sarah Spendlove, Wei Wang, Li Zhang, Yizhou Sun, Alex Bui, Henning Hermjakob, Karol E Watson, Peipei Ping

Affiliations

  1. The NIH BD2K Center of Excellence in Biomedical Computing, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  2. Department of Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  3. Department of Cardiology, First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, P.R. China.
  4. Department of Pediatric and Adult Congenital Cardiac Surgery, Miller Children's and Women's Hospital and Long Beach Memorial Hospital, Long Beach, CA 90806, USA.
  5. Department of Medicine/Cardiology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  6. Department of Bioinformatics, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  7. Department of Computer Science, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  8. Scalable Analytics Institute (ScAi), University of California at Los Angeles, Los Angeles, CA 90095, USA.
  9. Department of Radiological Sciences, University of California at Los Angeles, Los Angeles, CA 90095, USA.
  10. Molecular Systems Cluster, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

PMID: 30457569 PMCID: PMC6244181 DOI: 10.1038/sdata.2018.258

Abstract

Clinical case reports (CCRs) provide an important means of sharing clinical experiences about atypical disease phenotypes and new therapies. However, published case reports contain largely unstructured and heterogeneous clinical data, posing a challenge to mining relevant information. Current indexing approaches generally concern document-level features and have not been specifically designed for CCRs. To address this disparity, we developed a standardized metadata template and identified text corresponding to medical concepts within 3,100 curated CCRs spanning 15 disease groups and more than 750 reports of rare diseases. We also prepared a subset of metadata on reports on selected mitochondrial diseases and assigned ICD-10 diagnostic codes to each. The resulting resource, Metadata Acquired from Clinical Case Reports (MACCRs), contains text associated with high-level clinical concepts, including demographics, disease presentation, treatments, and outcomes for each report. Our template and MACCR set render CCRs more findable, accessible, interoperable, and reusable (FAIR) while serving as valuable resources for key user groups, including researchers, physician investigators, clinicians, data scientists, and those shaping government policies for clinical trials.

References

  1. J Am Soc Nephrol. 2013 Jul;24(8):1250-61 - PubMed
  2. Sci Rep. 2015 May 19;5:10021 - PubMed
  3. Am J Med Sci. 2007 Apr;333(4):226-9 - PubMed
  4. J Med Libr Assoc. 2016 Apr;104(2):146-9 - PubMed
  5. Nat Genet. 1996 Apr;12(4):385-9 - PubMed
  6. Ann Intern Med. 2001 Feb 20;134(4):330-4 - PubMed
  7. Bioinformatics. 2015 Jun 15;31(12):i339-47 - PubMed
  8. Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169 - PubMed
  9. IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92 - PubMed
  10. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):806-13 - PubMed
  11. Nephrol Dial Transplant. 2006 Apr;21(4):1104-8 - PubMed
  12. Am J Med Genet A. 2004 May 1;126A(4):349-54 - PubMed
  13. Circulation. 2011 Nov 8;124(19):2145-54 - PubMed
  14. Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617 - PubMed
  15. Nucleic Acids Res. 2015 Jan;43(Database issue):D1071-8 - PubMed
  16. BMC Res Notes. 2014 Apr 23;7:264 - PubMed
  17. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7415-9 - PubMed
  18. Sci Data. 2016 Mar 15;3:160018 - PubMed
  19. J Biomed Inform. 2014 Feb;47:1-10 - PubMed
  20. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D267-70 - PubMed
  21. BMC Res Notes. 2012 Jul 06;5:293 - PubMed
  22. BMC Bioinformatics. 2012 Jul 09;13:161 - PubMed
  23. Lancet. 2000 Sep 16;356(9234):1000-1 - PubMed
  24. J Neurol Sci. 1983 Dec;62(1-3):327-55 - PubMed
  25. J Biomed Inform. 2015 Dec;58 Suppl:S67-77 - PubMed
  26. J Neurol Neurosurg Psychiatry. 2002 Jul;73(1):82 - PubMed
  27. PLoS One. 2014 Oct 08;9(10):e109195 - PubMed
  28. Sci Data. 2018 Jun 12;5:180104 - PubMed
  29. Curr Cardiol Rep. 2014 Jul;16(7):501 - PubMed
  30. Clin Chem. 2003 Apr;49(4):624-33 - PubMed
  31. J Am Coll Cardiol. 2002 Jun 19;39(12):1890-900 - PubMed
  32. Sci Rep. 2018 May 9;8(1):7426 - PubMed
  33. Genet Med. 2017 Dec;19(12): - PubMed
  34. Nat Biotechnol. 2018 Aug;36(7):651-659 - PubMed
  35. Sci Data. 2018 Jan 30;5:180001 - PubMed
  36. Cancers (Basel). 2012 Nov 08;4(4):1180-211 - PubMed
  37. J R Soc Interface. 2018 Apr;15(141):null - PubMed
  38. J Am Med Inform Assoc. 2017 Nov 24;:null - PubMed
  39. Clin Chem. 2008 Feb;54(2):371-8 - PubMed
  40. Circ Cardiovasc Qual Outcomes. 2015 Sep;8(5):463-5 - PubMed
  41. J Biomed Inform. 2012 Aug;45(4):634-41 - PubMed
  42. J Am Med Inform Assoc. 2015 Sep;22(5):938-47 - PubMed
  43. Sci Rep. 2018 Apr 18;8(1):6193 - PubMed
  44. Genet Med. 2015 Sep;17(9):689-701 - PubMed
  45. Expert Rev Cardiovasc Ther. 2012 Nov;10(11):1401-11 - PubMed
  46. JRSM Short Rep. 2012 Dec;3(12):87 - PubMed
  47. Bioinformatics. 2014 Mar 15;30(6):868-75 - PubMed
  48. J Am Med Inform Assoc. 2010 Sep-Oct;17(5):507-13 - PubMed
  49. Sci Data. 2018 Jun 19;5:180111 - PubMed
  50. Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655 - PubMed

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