Term variation in clinical records First insights from a corpus study

Transcription

1 Term variation in clinical records First insights from a corpus study Séminaires du CENTAL 09 March 2018 Leonie Grön PhD candidate at Quantitative Lexicology and Variational Linguistics Supervised by Ann Bertels & Kris Heylen

2 UZ Leuven hospital supply patient records NLP in clinical workflow MARS Machine Reading of Patient Records QLVL linguistics terminological variation ICRI law privacy issues LIIR computer science semantic processing 2

3 Term variation??

4 hypertensie hypertension tensies verhoogd elevated tension?? hoge bloeddruk high blood pressure 4

5 witte jas hypertensie white coat hypertension lichte ht op rpl light ht during cnsl = light hypertension during consultation hier bd++ here bp++ = increase of blood pressure here (in the hospital setting) Onomasiological variation 5

6 creat verhoogd creat elevated = finding of an elevated creatinine level in a sample creat te doen creat to do = need to do a creatinine measurement for next consultation Semasiological variation 6

7 Why do we care?? patient profiling drug-drug interactions clinical decision support 7

8 high blood pressure HT 8

9 ... patient with HTN Hypertension... follow-up for BP Creatinine (substance)... creat elevated Creatinine measurement... creat to do... 9

10 Term variation!! I Which term types occur in clinical records? What are the processes underlying term alternations? II Which features can be linked to term variation? III Can those factors serve as predictive features for NLP? 10

11 I Types of terms and alternations 11

12 Variation between term types standardization lage bloedsuikers low blood sugars suikers aan de lage kant sugars in the low range hypoglycemie hypoglycemia hypo hypo (hypoglycemia) specialization 12

13 Distinction between formal term types 13

14 vernacular Formal term types standardization lage bloedsuikers low blood sugars suikers aan de lage kant sugars in the low range hypoglycemie hypoglycemia hypo hypo (hypoglycemia) specialization 14

15 Formal term types standardization lage bloedsuikers low blood sugars colloquial suikers aan de lage kant sugars in the low range hypoglycemie hypoglycemia hypo hypo (hypoglycemia) specialization 15

16 standard specialized Formal term types standardization lage bloedsuikers low blood sugars suikers aan de lage kant sugars in the low range hypoglycemie hypoglycemia hypo hypo (hypoglycemia) specialization 16

17 Formal term types standardization lage bloedsuikers low blood sugars suikers aan de lage kant sugars in the low range clinical jargon hypoglycemie hypoglycemia hypo hypo (hypoglycemia) specialization 17

18 Variation processes at different levels 18

19 phraseal derivation by affixation malleolus malleolair at the ankle lexical morphological syndroom van Cushin cushinoïd indicative of Cushin s syndrome (hormonal disorder) compositions buikpijn buikpijnklachten complaints of stomach ache 19

20 phraseal lexical morphological abbreviations elektrokardiografie EKG electrocardiography NovoRapid NR insulin product malleolair mall at the ankle schildklierfunctie skfie function of the thyroid gland 20

21 phraseal lexical alternation between vernacular/ specialized lexemes hartauscultatie corauscultatie listening to the sounds of the heart blaasontsteking cystitis inflammation of the bladder morphological 21

22 phraseal lexical structure of multi-word units hypertrofie van de nagels hypertrofische nagels thickened nails cerebrale angiografie angio hersenen examination of the blood vessels of the brain morphological 22

23 II Systematic analysis: Corpus study 23

24 electronic health records 500 patients with diabetes composed with semi-structured template selected sections are merged into a discharge letter Complaints Anamnesis Lab reports Conclusion 24

25 well-formedness anamnesis complaints clinical conclusion lab reports proportion of specialized information 25

26 well-formedness anamnesis complaints clinical conclusion lab reports proportion of specialized information 26

27 well-formedness anamnesis complaints clinical conclusion lab reports proportion of specialized information 27

28 well-formedness anamnesis complaints clinical conclusion lab reports proportion of specialized information 28

29 well-formedness anamnesis complaints clinical conclusion lab reports proportion of specialized information 29

30 annotators: 5 students of biomedical sciences terminology: local version of SNOMED-CT(Dutch) task: annotate all medical terms include non-standard forms Annotation procedure multi-word expressions: use the most comprehensive code available SCTID SCTID SCTID angiography of neck NOT: angiography, neck 30

31 Manual annotationwith concept codes from the clinical ontology SNOMED-CT 31

32 Unknown variants: Consult the SNOMED-CT online browser 32

33 Commercial drug names: Look up active substance in the drug compendium and map to SNOMED-CT concept 33

34 Annotation output medical histories of ~180 patients ~ terms in total unique terms unique concepts 34

35 General statistics 1) distribution across the report sections 2) proportion of term types 3) proportion of semantic classes Scope of variation 1) concept-to-term ratio 2) term-to-concept ratio Factors influencing term selection 1) conceptual features ~ term type 2) sectionwithin the document ~ term type 35

36 General statistics 36

37 1) distribution across sections Retrieve the original section based on position of the annotated span Complaints Anamnesis Lab reports Conclusion Sort terms by section 2x hypertension, 1x foot 5x blood, 3x iron Calculate the proportion relative to the total number of identified terms 37

38 1) distribution across sections section proportion of terms in % clinical conclusion medical history patient's complaints 3.07 medication 2.31 physical examination 1.81 comments 1.21 anamnesis

39 2) Proportion of term types Annotation with features describing the degree of specialization and standardization Calculation of the proportion of term types standardization vernacular colloquial standard specialized jargon specialization 39

40 2) proportion of term types term type proportion of entities in % vernacular specialized standard clinical jargon colloquial

41 3) proportion of semantic classes Mapping to concepts of the UMLS Metathesaurus inheritance of semantic labels Absolute frequencies by semantic classes 41

42 disorders Diseases diabetes mellitus type 2 Symptoms fatigue Injuries burn, cut 42

43 procedures Diagnostic Therapeutic Preventive heart auscultation gastroplasty dietary education 43

44 concepts & ideas Qualitative Spatial Temporal proliferative, high right side, bilateral at noon, postprandial 44

45 chemicals & drugs Clinical drugs aspirine Hormones estrogen Vitamines vitamin b12 45

46 anatomy Body parts arm, kidney Regions head and neck Cells plasma cel 46

47 living beings Humans patient, hematologist Bacteria streptococcus 47

48 physiology Organ function peristalsis Cell function beta-cell function Cognitive ability memory 48

49 phenomena Test result lowering of blood glucose level Natural forces heat Human-induced events accident 49

50 Scope of variation 50

51 1) concept-to-term ratio calculate the number of unique terms used to express one concept high number of variants ~ onomasiologicalvariation 2) term-to-concept ratio calculate the number of concepts associated with one term high number of concepts ~ semasiologicalvariation 51

52 1) concept-to-term ratio Preferred term in SNOMED number of variants example semantic type Change in insulin dose 103 Patient feels well 95 High glucose level in blood 78 General health good 73 aanpassingen gedaan made adjustments klachtenvrij free from complaints schommelende waardes fluctuating values goede algemene conditie good general condition procedures > therapeutic disorders > finding disorders > finding disorders > finding Chest auscultation finding 71 cor/longen normaal heart/lungs normal disorders > finding 52

53 Onomasiological variation ~ conceptual properties fuzzy and less specialized concepts procedures carried out by the patient subjective findings high number of term variants physical entities and medically defined concepts anatomy diagnoses of diseases lownumber of term variants 53

54 2) term-to-concept ratio term number of concepts preferred terms ofconcepts in SNOMED semantic classes of concepts cor 10 abdomen 10 heart examination of heart examination of abdomen abdominal test finding anatomy, procedures, phenomena, disorders anatomy, procedures, physiology, disorders pols 8 of 7 creat 7 pulse rate pulse function ophthalmological and optical investigations eye examination creatine measurement finding of creatine kinase level anatomy, procedures, physiology, disorders procedures, occupations chemicals & drugs, procedures, disorders 54

55 Semasiological variation ~ conceptualproperties + frequency entitiesthat are object of routine examination anatomical concepts physiological functions organic substances use of reduced, ambiguous forms highnumber of concept links 55

56 Factors influencing term selection 56

57 1) influence of conceptual properties proportion of term types by semantic class 100% 75% 50% 25% 0% disorders procedures anatomy phenomena clinical jargon standard specialized terms vernacular colloquial 57

58 2) Influence of formal context Proportion of term types by report sections 100% 80% 60% 40% 20% 0% conclusion complaints examination lab report specialized clinical jargon vernacular colloquial 58

59 Preferences for term types specialization ~ conceptual and pragmatic factors tangible entities basic anatomy patient-centred sections complaints non-specialized less accessible concepts hematological parameters sections based on clinical assessment examination specialized 59

60 Preferences for term types standardization~ pragmatic factors addressed at external readers conclusion standard intended for internal use lab reports non-standard 60

61 III Conclusions 61

62 Term variation is ubiquitous in clinical documentation affects all levels of language processing patterns with conceptual properties pragmatic factors can improve the design of NLP systems 62

63 Thank you for your attention! Questions? Suggestions? 63