title: A complementary graphical method for reducing and analyzing large data sets. Case studies demonstrating thresholds setting and selection.
abstract: OBJECTIVE
  Graphical displays can make data more understandable; however, large graphs can challenge human comprehension. We have previously described a filtering method to provide high-level summary views of large data sets. In this paper we demonstrate our method for setting and selecting thresholds to limit graph size while retaining important information by applying it to large single and paired data sets, taken from patient and bibliographic databases.
  
  
  METHODS
  Four case studies are used to illustrate our method. The data are either patient discharge diagnoses (coded using the International Classification of Diseases, Clinical Modifications [ICD9-CM]) or Medline citations (coded using the Medical Subject Headings [MeSH]). We use combinations of different thresholds to obtain filtered graphs for detailed analysis. The thresholds setting and selection, such as thresholds for node counts, class counts, ratio values, p values (for diff data sets), and percentiles of selected class count thresholds, are demonstrated with details in case studies. The main steps include: data preparation, data manipulation, computation, and threshold selection and visualization. We also describe the data models for different types of thresholds and the considerations for thresholds selection.
  
  
  RESULTS
  The filtered graphs are 1%-3% of the size of the original graphs. For our case studies, the graphs provide 1) the most heavily used ICD9-CM codes, 2) the codes with most patients in a research hospital in 2011, 3) a profile of publications on "heavily represented topics" in MEDLINE in 2011, and 4) validated knowledge about adverse effects of the medication of rosiglitazone and new interesting areas in the ICD9-CM hierarchy associated with patients taking the medication of pioglitazone.
  
  
  CONCLUSIONS
  Our filtering method reduces large graphs to a manageable size by removing relatively unimportant nodes. The graphical method provides summary views based on computation of usage frequency and semantic context of hierarchical terminology. The method is applicable to large data sets (such as a hundred thousand records or more) and can be used to generate new hypotheses from data sets coded with hierarchical terminologies.
authors.affiliation: Xia Jing, Assistant Professor, NIH Clinical Center, National Institutes of Health, Street, Bethesda, MA, USA.
authors.forename: X
authors.initials: X
authors.lastname: Jing
authors.forename: J J
authors.initials: JJ
authors.lastname: Cimino
mesh_terms: D000465:Algorithms; D059019:Clinical Coding; D003196:Computer Graphics; D003626:Data Display; D066264:Datasets as Topic; D001330:Electronic Data Processing; D057286:Electronic Health Records / Q000706:statistics & numerical data*; D006801:Humans; D038801:International Classification of Diseases; D008492:Medical Informatics Computing; D010351:Patient Discharge; D000077205:Pioglitazone; D009626:Terminology as Topic; D045162:Thiazolidinediones / Q000009:adverse effects / Q000627:therapeutic use
chemical_list: D045162:Thiazolidinediones; D000077205:Pioglitazone
keywords: Data mining method; clinical data repository; data analysis; data filtering method; data visualization; hierarchical terminology; threshold selection; threshold setting
references.citation: PLoS One. 2012;7(3):e33812
references.pmid: 22479449
references.citation: Int J Funct Inform Personal Med. 2010;3(4):273-291
references.pmid: 22899966
references.citation: AMIA Annu Symp Proc. 2011;2011:635-43
references.pmid: 22195119
references.citation: Diabetes Care. 2010 Mar;33(3):526-31
references.pmid: 20009093
references.citation: Crit Care Med. 2011 May;39(5):952-60
references.pmid: 21283005
references.citation: Methods Inf Med. 2013;52(1):43-50
references.pmid: 23223709
references.citation: Stud Health Technol Inform. 2010;160(Pt 2):1299-303
references.pmid: 20841894
references.citation: Methods Inf Med. 2002;41(5):411-3
references.pmid: 12501813
references.citation: Methods Inf Med. 1993 Aug;32(4):281-91
references.pmid: 8412823
references.citation: J Am Med Inform Assoc. 2010 Mar-Apr;17(2):124-30
references.pmid: 20190053