| Literature DB >> 30975223 |
Mike Conway1, Salomeh Keyhani2,3, Lee Christensen4, Brett R South4,5, Marzieh Vali2, Louise C Walter2,3, Danielle L Mowery4,5, Samir Abdelrahman4, Wendy W Chapman4,5.
Abstract
BACKGROUND: Social risk factors are important dimensions of health and are linked to access to care, quality of life, health outcomes and life expectancy. However, in the Electronic Health Record, data related to many social risk factors are primarily recorded in free-text clinical notes, rather than as more readily computable structured data, and hence cannot currently be easily incorporated into automated assessments of health. In this paper, we present Moonstone, a new, highly configurable rule-based clinical natural language processing system designed to automatically extract information that requires inferencing from clinical notes. Our initial use case for the tool is focused on the automatic extraction of social risk factor information - in this case, housing situation, living alone, and social support - from clinical notes. Nursing notes, social work notes, emergency room physician notes, primary care notes, hospital admission notes, and discharge summaries, all derived from the Veterans Health Administration, were used for algorithm development and evaluation.Entities:
Keywords: Natural language processing; Social determinants of health; Software
Mesh:
Year: 2019 PMID: 30975223 PMCID: PMC6458709 DOI: 10.1186/s13326-019-0198-0
Source DB: PubMed Journal: J Biomed Semantics
Fig. 1System architecture. Ovals (green) are knowledge resources, and rectangles (blue) are Moonstone components
Fig. 2TSL example
Fig. 3Semantic grammar rule
Fig. 4Word-level grammar rule mapping phrases to normalizing constant “:SPOUSE:”. Note that these rules were defined for the US healthcare system and hence may not prove appropriate for non-US contexts
Fig. 5TSL rule used to augment grammatical analysis
Fig. 6Parse tree for “patient lives with his wife at home”
Mention level classification results
|
| TPa | FPb | FNc | Send | NPVe | PPVf | Accg | F-scoreh |
|---|---|---|---|---|---|---|---|---|
|
| ||||||||
| Homeless/marginally housed | 79 | 39 | 11 | 0.87 | 0.38 | 0.66 | 0.63 | 0.75 |
| Lives at home/not homeless | 6382 | 111 | 335 | 0.95 | 0.02 | 0.98 | 0.93 | 0.96 |
| Lives in a facility | 426 | 131 | 141 | 0.75 | 0.26 | 0.76 | 0.63 | 0.75 |
|
| ||||||||
| Does not live alone | 1329 | 123 | 88 | 0.93 | 0.11 | 0.91 | 0.86 | 0.92 |
| Lives alone | 710 | 19 | 17 | 0.97 | 0.05 | 0.97 | 0.95 | 0.97 |
|
| ||||||||
| Has social support | 5174 | 525 | 337 | 0.93 | 0.21 | 0.90 | 0.85 | 0.92 |
| No social support | 220 | 59 | 19 | 0.92 | 0.78 | 0.78 | 0.78 | 0.84 |
aTrue positive
bFalse positive
cFalse negative
dSensitivity (i.e. recall)
eNegative predictive value
fPositive predictive value (i.e. precision)
gAccuracy
hF-score (harmonic mean of positive predictive value and sensitivity)
Proportion of direct grammar rules used per category
| Concept | Proportion of direct grammar rules utilized |
|---|---|
| Lives Alone | 25.0% |
| Does Not Live Alone | 0.6% |
| Has Social Support | 4.8% |
| Lacks Social Support | 20.0% |
| Not homeless/lives at home | 5.8% |
| Homeless/marginally housed | 80.5% |
| Lives In Facility (e.g. nursing home) | 0.0% |