Mapping the categories of the Swedish primary health care version of ICD-10 to SNOMED CT concepts: Rule development and intercoder reliability in a mapping trial

<p>Abstract</p> <p>Background</p> <p>Terminologies and classifications are used for different purposes and have different structures and content. Linking or mapping terminologies and classifications has been pointed out as a possible way to achieve various aims as well as to attain additional advantages in describing and documenting health care data.</p> <p>The objectives of this study were:</p> <p>• to explore and develop rules to be used in a mapping process</p> <p>• to evaluate intercoder reliability and the assessed degree of concordance when the 'Swedish primary health care version of the International Classification of Diseases version 10' (ICD-10) is matched to the Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT)</p> <p>• to describe characteristics in the coding systems that are related to obstacles to high quality mapping.</p> <p>Methods</p> <p>Mapping (interpretation, matching, assessment and rule development) was done by two coders. The Swedish primary health care version of ICD-10 with 972 codes was randomly divided into an allotment of three sets of categories, used in three mapping sequences, A, B and C. Mapping was done independently by the coders and new rules were developed between the sequences. Intercoder reliability was measured by comparing the results after each set. The extent of matching was assessed as either 'partly' or 'completely concordant'</p> <p>Results</p> <p>General principles for mapping were outlined before the first sequence, A. New mapping rules had significant impact on the results between sequences A - B (p < 0.01) and A - C (p < 0.001). The intercoder reliability in our study reached 83%. Obstacles to high quality mapping were mainly a lack of agreement by the coders due to structural and content factors in SNOMED CT and in the current ICD-10 version. The predominant reasons for this were difficulties in interpreting the meaning of the categories in the current ICD-10 version, and the presence of many related concepts in SNOMED CT.</p> <p>Conclusion</p> <p>Mapping from ICD-10-categories to SNOMED CT needs clear and extensive rules. It is possible to reach high intercoder reliability in mapping from ICD-10-categories to SNOMED CT. However, several obstacles to high quality mapping remain due to structure and content characteristics in both coding systems.</p

Formal representation of complex SNOMED CT expressions

<p>Abstract</p> <p>Background</p> <p>Definitory expressions about clinical procedures, findings and diseases constitute a major benefit of a formally founded clinical reference terminology which is ontologically sound and suited for formal reasoning. SNOMED CT claims to support formal reasoning by description-logic based concept definitions.</p> <p>Methods</p> <p>On the basis of formal ontology criteria we analyze complex SNOMED CT concepts, such as "Concussion of Brain with(out) Loss of Consciousness", using alternatively full first order logics and the description logic <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1472-6947-8-S1-S9-i1"><m:semantics><m:mrow><m:mi>ℰ</m:mi><m:mi>ℒ</m:mi></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae8hmHuKae8NeHWeaaa@37B1@</m:annotation></m:semantics></m:math></inline-formula>.</p> <p>Results</p> <p>Typical complex SNOMED CT concepts, including negations or not, can be expressed in full first-order logics. Negations cannot be properly expressed in the description logic <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1472-6947-8-S1-S9-i1"><m:semantics><m:mrow><m:mi>ℰ</m:mi><m:mi>ℒ</m:mi></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae8hmHuKae8NeHWeaaa@37B1@</m:annotation></m:semantics></m:math></inline-formula> underlying SNOMED CT. All concepts concepts the meaning of which implies a temporal scope may be subject to diverging interpretations, which are often unclear in SNOMED CT as their contextual determinants are not made explicit.</p> <p>Conclusion</p> <p>The description of complex medical occurrents is ambiguous, as the same situations can be described as (i) a complex occurrent <it>C </it>that has <it>A </it>and <it>B </it>as temporal parts, (ii) a simple occurrent <it>A' </it>defined as a kind of A followed by some <it>B</it>, or (iii) a simple occurrent <it>B' </it>defined as a kind of <it>B </it>preceded by some <it>A</it>. As negative statements in SNOMED CT cannot be exactly represented without a (computationally costly) extension of the set of logical constructors, a solution can be the reification of negative statments (e.g., "Period with no Loss of Consciousness"), or the use of the SNOMED CT context model. However, the interpretation of SNOMED CT context model concepts as description logics axioms is not recommended, because this may entail unintended models.</p

Representing SNOMED CT Concept Evolutions using Process Profiles

Abstract. SNOMED CT is a very large biomedical terminology supported by a concept-based ontology. In recent years it has been distributed under the new release format &apos;RF2&apos;. RF2 provides a more consistent and coherent mechanism for keeping track of changes over versions, even to the extent that -in theory at leastany release will contain enough information to allow reconstruction of all previous versions. In this paper, using the January 2016 release of SNOMED CT, we explore various ways to transform change-assertions in RF2 into a more uniform representation with the goal of assessing how faithful these changes are with respect to biomedical reality. Key elements in our approach are (1) recent proposals for the Information Artifact Ontology that provide a realism-based perspective on what it means for a representation to be about something, and (2) the expectation that the theory of what we call &apos;process profiles&apos; can be applied not merely to quantitative information artifacts but also to other sorts of symbolic representations of processes

Automation of a problem list using natural language processing

BACKGROUND: The medical problem list is an important part of the electronic medical record in development in our institution. To serve the functions it is designed for, the problem list has to be as accurate and timely as possible. However, the current problem list is usually incomplete and inaccurate, and is often totally unused. To alleviate this issue, we are building an environment where the problem list can be easily and effectively maintained. METHODS: For this project, 80 medical problems were selected for their frequency of use in our future clinical field of evaluation (cardiovascular). We have developed an Automated Problem List system composed of two main components: a background and a foreground application. The background application uses Natural Language Processing (NLP) to harvest potential problem list entries from the list of 80 targeted problems detected in the multiple free-text electronic documents available in our electronic medical record. These proposed medical problems drive the foreground application designed for management of the problem list. Within this application, the extracted problems are proposed to the physicians for addition to the official problem list. RESULTS: The set of 80 targeted medical problems selected for this project covered about 5% of all possible diagnoses coded in ICD-9-CM in our study population (cardiovascular adult inpatients), but about 64% of all instances of these coded diagnoses. The system contains algorithms to detect first document sections, then sentences within these sections, and finally potential problems within the sentences. The initial evaluation of the section and sentence detection algorithms demonstrated a sensitivity and positive predictive value of 100% when detecting sections, and a sensitivity of 89% and a positive predictive value of 94% when detecting sentences. CONCLUSION: The global aim of our project is to automate the process of creating and maintaining a problem list for hospitalized patients and thereby help to guarantee the timeliness, accuracy and completeness of this information

Microscopic colitis : epidemiology, death and associated disorders

Microscopic colitis (MC) is the most recently recognized inflammatory condition of the large intestine. MC is an umbrella term for two disease entities, namely lymphocytic colitis (LC) and collagenous colitis (CC). These subtypes are distinguished by their histopathological presentation and cannot be separated based on clinical observation or symptoms. The most prominent clinical presentation is watery, non-bloody diarrhea. However, a proportion of patients also suffer from abdominal pain, weight loss, fecal incontinence and reduced quality of life. MC primarily affects the elderly and shows a clear female preponderance with some 2/3 of patients being women. Large scale, epidemiological research of the disease has historically been hampered by insufficient awareness. Therefore, using data from Swedish health care registers, this thesis aims to elucidate temporal patterns of MC as well as the association with mortality, cancer and celiac disease (CD). In study I, we examined the validity of having a MC diagnosis recorded in Swedish regional pathology registers. Through manual review of medical charts (n=211), carried out by two independent reviewers, we computed a positive predictive value for MC of 95%. Thus, we concluded that Swedish pathology registers are a reliable source for identifying patients with MC. In study II, we identified every patient with a first-time diagnosis of MC recorded in Swedish pathology registers from 1995-2015. Using this cohort, we examined temporal trends, age distribution and sex differences in MC. As expected, a majority of patients (72%) were female and mean age at diagnosis was 60.2 years. Incidence rates increased appreciably from 1995 to 2012, after which rates have stabilized. The mean age-standardized incidence rate from 2006 to 2015 was 10.5 cases/100,000 person-years, with a female to male incidence rate ratio of 2.4, adjusted for age and calendar period. When analyzing age-specific incidence, incidence rates increased up to 75-79 years after which they declined. Furthermore, we estimated that during a life-time 1 in 115 women and 1 in 286 men are expected to be diagnosed with MC. In study III we examined mortality in patients with MC. This was done using a matched cohort study design where each exposed individual (MC) (n=14,333) was matched according to age, sex, county of residence and year of biopsy to five reference individuals from the general population. During the study period (1990 to 2017) patients with MC had a higher probability of death. However, after adjustment for comorbidities the association vanished. Thus, we concluded that the increased risk of death is attributable to the burden of concomitant disease. Study IV aimed to investigate the association between MC and cancer. Again, this was done using the matched cohort design described above. In total, we identified 11,758 patients diagnosed with MC between 1990 and 2016 with MC that were matched to 50,828 reference individuals. After adjustments for the matching variables and comorbidities (CD and diabetes), we estimated an adjusted hazard ratio (aHR) of 1.08 (95%CI=1.02-1.16) for overall cancer. In secondary analyses, we found a decreased probability of colorectal cancer (aHR, 0.52 (95%CI_0.40-0.66)). The same pattern was observed for gastrointestinal cancers overall (aHR, 0.72(95%CI=0.60-0.85)). In study V we examined the association between CD and MC. Using the same matched cohort study design described above, we identified 45,267 patients with CD and 224,568 reference individuals between 1990 and 2016. 456 patients with CD were diagnosed with MC during the study period compared to 198 reference individuals that developed MC during the same period. These figures correspond to an aHR of 11.5 (95%CI=9.3-13.7). However, as the proportional hazards assumption was violated, the main result should not be interpreted as the probability for a CD patient to develop MC at any instant during the study period compared to the reference population, but rather a mean aHR based on all lengths of follow up. However, as the increased risk remained even after >10 years of follow up, our results indicate that the concomitance of these diagnoses should be considered if symptoms persist or reoccur despite a gluten free diet

Variation in patient pathways and hospital admissions for exacerbations of COPD: linking the National COPD Audit with CPRD data

The aim of this thesis was to link secondary care data from a UK national audit of chronic obstructive pulmonary disease (COPD) care with primary care data from a database of UK electronic health records (EHRs) to explore how variations in patient pathways through healthcare across England affect hospital admissions for acute exacerbations of COPD (AECOPD). This aim was achieved through 6 objectives: (i) a systematic review of the literature on validation of AECOPD definitions in EHRs; (ii) determination of predictors of referral to pulmonary rehabilitation from general practice; (iii) a comparison of the quality of COPD primary care in each UK country, as currently only Wales is assessed; (iv) determination of whether the COPD Best Practice Tariff (BPT) pay-for-performance scheme improves patient outcomes; (v) assessment of the utility of NEWS2 as a severity score measure in AECOPD admissions; (vi) linkage of secondary care audit data with primary care EHR data to explore how management of patients with COPD affects AECOPD hospital admissions. A summary of the key results is as follows. Firstly, although few studies have validated AECOPD definitions, a validated AECOPD definition was found in a systematic search of the literature that could be used in subsequent objectives. Secondly. while generally appropriate patients appear to be prioritised for PR referral, women were less likely to be considered for referral than men. Thirdly, England, Scotland, and Northern Ireland had substantially lower proportions of patients with confirmed airways obstruction and referrals to pulmonary rehabilitation than Wales. This suggests that completing primary care audits solely in Wales is leading to improvements in, at least, the recording of care that are not happening in the rest of the UK. Fourthly, the combination of interventions financially incentivised by the COPT BPT were not associated with an improvement in 30-day mortality or readmission. One component of the BPT, specialist review, was associated with 31% lower odds of inpatient mortality. Fifthly, NEWS2 was a poor predictor of length of hospital stay, requirement for NIV, and inpatient mortality, with AUC values of 0.7 or less for each outcome. Sixth and finally, 80% of patients admitted for AECOPD had contact with their GP in the 2 weeks prior to admission, suggesting that these admissions could not have been avoided. 86% of admissions were clinically appropriate. Contact with primary care did not appear to affect admission appropriateness. Receipt of a discharge care bundle was associated with receipt of best practice care, however this association appeared to derive from already having received those items of care in secondary care. Power was limited in the final analyses making it difficult to draw firm conclusions, however COPD discharge care bundles do not appear to be leading to improvements in key patient outcomes.Open Acces

Generating Reliable and Responsive Observational Evidence: Reducing Pre-analysis Bias

A growing body of evidence generated from observational data has demonstrated the potential to influence decision-making and improve patient outcomes. For observational evidence to be actionable, however, it must be generated reliably and in a timely manner. Large distributed observational data networks enable research on diverse patient populations at scale and develop new sound methods to improve reproducibility and robustness of real-world evidence. Nevertheless, the problems of generalizability, portability and scalability persist and compound. As analytical methods only partially address bias, reliable observational research (especially in networks) must address the bias at the design stage (i.e., pre-analysis bias) including the strategies for identifying patients of interest and defining comparators. This thesis synthesizes and enumerates a set of challenges to addressing pre-analysis bias in observational studies and presents mixed-methods approaches and informatics solutions for overcoming a number of those obstacles. We develop frameworks, methods and tools for scalable and reliable phenotyping including data source granularity estimation, comprehensive concept set selection, index date specification, and structured data-based patient review for phenotype evaluation. We cover the research on potential bias in the unexposed comparator definition including systematic background rates estimation and interpretation, and definition and evaluation of the unexposed comparator. We propose that the use of standardized approaches and methods as described in this thesis not only improves reliability but also increases responsiveness of observational evidence. To test this hypothesis, we designed and piloted a Data Consult Service - a service that generates new on-demand evidence at the bedside. We demonstrate that it is feasible to generate reliable evidence to address clinicians’ information needs in a robust and timely fashion and provide our analysis of the current limitations and future steps needed to scale such a service