A UMLS-based spell checker for natural language processing in vaccine safety

BACKGROUND: The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. METHODS: We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. RESULTS: We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74–75), 100% (95% CI: 100–100), and 47% (95% CI: 46%–48%), respectively. CONCLUSION: We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest

INSPIRE (INvestigating Social and PractIcal suppoRts at the End of life): Pilot randomised trial of a community social and practical support intervention for adults with life-limiting illness

YesBACKGROUND: For most people, home is the preferred place of care and death. Despite the development of specialist palliative care and primary care models of community based service delivery, people who are dying, and their families/carers, can experience isolation, feel excluded from social circles and distanced from their communities. Loneliness and social isolation can have a detrimental impact on both health and quality of life. Internationally, models of social and practical support at the end of life are gaining momentum as a result of the Compassionate Communities movement. These models have not yet been subjected to rigorous evaluation. The aims of the study described in this protocol are: (1) to evaluate the feasibility, acceptability and potential effectiveness of The Good Neighbour Partnership (GNP), a new volunteer-led model of social and practical care/support for community dwelling adults in Ireland who are living with advanced life-limiting illness; and (2) to pilot the method for a Phase III Randomised Controlled Trial (RCT). DESIGN: The INSPIRE study will be conducted within the Medical Research Council (MRC) Framework for the Evaluation of Complex Interventions (Phases 0-2) and includes an exploratory two-arm delayed intervention randomised controlled trial. Eighty patients and/or their carers will be randomly allocated to one of two groups: (I) Intervention: GNP in addition to standard care or (II) Control: Standard Care. Recipients of the GNP will be asked for their views on participating in both the study and the intervention. Quantitative and qualitative data will be gathered from both groups over eight weeks through face-to-face interviews which will be conducted before, during and after the intervention. The primary outcome is the effect of the intervention on social and practical need. Secondary outcomes are quality of life, loneliness, social support, social capital, unscheduled health service utilisation, caregiver burden, adverse impacts, and satisfaction with intervention. Volunteers engaged in the GNP will also be assessed in terms of their death anxiety, death self efficacy, self-reported knowledge and confidence with eleven skills considered necessary to be effective GNP volunteers. DISCUSSION: The INSPIRE study addresses an important knowledge gap, providing evidence on the efficacy, utility and acceptability of a unique model of social and practical support for people living at home, with advanced life-limiting illness. The findings will be important in informing the development (and evaluation) of similar service models and policy elsewhere both nationally and internationally. TRIAL REGISTRATION: ISRCTN18400594 18(th) February 2015

Reliability and Validity of the Modified Colorado Symptom Index within a National Homeless Population

This study examined the reliability and construct validity of a modified version of the Colorado Symptom Index (MCSI), a brief, self-report measure of psychological symptomatology, in a study of interventions to prevent homelessness. Eight projects in a national, cooperative study collected new data at baseline, 6, and 12 months using a set of common measures as well as site-specific instruments. The pooled sample consisted of 1,381 persons in treatment for mental illness or substance abuse (or both), of which 84% had a history of homelessness. The analyses employed classical and Rasch methods to examine the MCSI\u27s content validity, internal consistency and item quality, test/retest reliability, dimensionality, appropriateness for the sample, construct validity, and responsiveness to change. This 14-item scale was found to be a reliable and valid measure of psychological symptoms in this sample. Its content was consistent with other symptom measures, its high internal consistency and test-retest coefficients supported its reliability, its relationships to other measures indicated that it had good construct validity, and it was responsive to change. We conclude that the MCSI performed similarly to longer, more widely used measures of psychological symptomatology and could be useful in other studies targeting homeless adults with severe mental illness, substance use disorders, or both

BMC Medical Informatics and Decision Making 2007, 7:3 doi:10.1186/1472-6947-7-3

Research article A UMLS-based spell checker for natural language processing in vaccine safet