Getting the foot out of the pelvis: modeling problems affecting use of SNOMED CT hierarchies in practical applications

Objectives

(a) To determine the extent and range of errors and issues in the Systematised Nomenclature of Medicine – Clinical Terms (SNOMED CT) hierarchies as they affect two practical projects. (b) To determine the origin of issues raised and propose methods to address them.

Methods

The hierarchies for concepts in the Core Problem List Subset published by the Unified Medical Language System were examined for their appropriateness in two applications. Anomalies were traced to their source to determine whether they were simple local errors, systematic inferences propagated by SNOMED''s classification process, or the result of problems with SNOMED''s schemas. Conclusions were confirmed by showing that altering the root cause and reclassifying had the intended effects, and not others.

Main results

Major problems were encountered, involving concepts central to medicine including myocardial infarction, diabetes, and hypertension. Most of the issues raised were systematic. Some exposed fundamental errors in SNOMED''s schemas, particularly with regards to anatomy. In many cases, the root cause could only be identified and corrected with the aid of a classifier.

Limitations

This is a preliminary ‘experiment of opportunity.’ The results are not exhaustive; nor is consensus on all points definitive.

Conclusions

The SNOMED CT hierarchies cannot be relied upon in their present state in our applications. However, systematic quality assurance and correction are possible and practical but require sound techniques analogous to software engineering and combined lexical and semantic techniques. Until this is done, anyone using SNOMED codes should exercise caution. Errors in the hierarchies, or attempts to compensate for them, are likely to compromise interoperability and meaningful use.     

Using SNOMED CT to Represent Two Interface Terminologies

Objective

Interface terminologies are designed to support interactions between humans and structured medical information. In particular, many interface terminologies have been developed for structured computer based documentation systems. Experts and policy-makers have recommended that interface terminologies be mapped to reference terminologies. The goal of the current study was to evaluate how well the reference terminology SNOMED CT could map to and represent two interface terminologies, MEDCIN and the Categorical Health Information Structured Lexicon (CHISL).

Design

Automated mappings between SNOMED CT and 500 terms from each of the two interface terminologies were evaluated by human reviewers, who also searched SNOMED CT to identify better mappings when this was judged to be necessary. Reviewers judged whether they believed the interface terms to be clinically appropriate, whether the terms were covered by SNOMED CT concepts and whether the terms' implied semantic structure could be represented by SNOMED CT.

Measurements

Outcomes included concept coverage by SNOMED CT for study terms and their implied semantics. Agreement statistics and compositionality measures were calculated.

Results

The SNOMED CT terminology contained concepts to represent 92.4% of MEDCIN and 95.9% of CHISL terms. Semantic structures implied by study terms were less well covered, with some complex compositional expressions requiring semantics not present in SNOMED CT. Among sampled terms, those from MEDCIN were more complex than those from CHISL, containing an average 3.8 versus 1.8 atomic concepts respectively, p<0.001.

Conclusion

Our findings support using SNOMED CT to provide standardized representations of information created using these two terminologies, but suggest that enriching SNOMED CT semantics would improve representation of the external terms.     

Migrating existing clinical content from ICD-9 to SNOMED

Objective

To identify challenges in mapping internal International Classification of Disease, 9th edition, Clinical Modification (ICD-9-CM) encoded legacy data to Systematic Nomenclature of Medicine (SNOMED), using SNOMED-prescribed compositional approaches where appropriate, and to explore the mapping coverage provided by the US National Library of Medicine (NLM)''s SNOMED clinical core subset.

Design

This study selected ICD-CM codes that occurred at least 100 times in the organization''s problem list or diagnosis data in 2008. After eliminating codes whose exact mappings were already available in UMLS, the remainder were mapped manually with software assistance.

Results

Of the 2194 codes, 784 (35.7%) required manual mapping. 435 of these represented concept types documented in SNOMED as deprecated: these included the qualifying phrases such as ‘not elsewhere classified’. A third of the codes were composite, requiring multiple SNOMED code to map. Representing 45 composite concepts required introducing disjunction (‘or’) or set-difference (‘without’) operators, which are not currently defined in SNOMED. Only 47% of the concepts required for composition were present in the clinical core subset. Search of SNOMED for the correct concepts often required extensive application of knowledge of both English and medical synonymy.

Conclusion

Strategies to deal with legacy ICD data must address the issue of codes created by non-taxonomist users. The NLM core subset possibly needs augmentation with concepts from certain SNOMED hierarchies, notably qualifiers, body structures, substances/products and organisms. Concept-matching software needs to utilize query expansion strategies, but these may be effective in production settings only if a large but non-redundant SNOMED subset that minimizes the proportion of extensively pre-coordinated concepts is also available.     

Computed Tomographic Findings in 50 Cases of Gall Bladder Carcinoma

Background

A retrospective assessment of contrast enhanced computed tomography (CECT) scan findings in histopathologically proven cases of carcinoma of the gallbladder (GB) was performed to review its role in diagnosis, staging and assessment of surgical resectability.

Methods

All the patients had been subjected to a standardised abdominal helical computed tomography scan. Orally administered iodinated contrast was used for opacification of bowel and dynamic intravenous injection of non-ionic iodinated contrast for studying the lesional enhancement and vascular structures.

Results

The presence of focal or diffuse mass lesions in the gallbladder fossa, infiltration of a liver and second part of duodenum were the most reliable diagnostic features in carcinoma gallbladder. Regional spread was better delineated on CT scan as compared with ultrasonography.

Conclusion

CT scan is an effective method for evaluating, characterizing and detecting the spread of GB carcinomas.Key Words: Gall Bladder, Carcinoma, Computed Tomography     

Increased serum nitric oxide and malondialdehyde levels in patients with acute intestinal amebiasis

Objective

To determine the level of oxygen-nitrogen stress parameters in the pathogenesis of amebiasis.

Methods

Twenty-four acute intestinal amebiasis patients and 20 healthy controls were enrolled in the present study. Serum malondialdehyde and nitric oxide levels were determined spectrophotometrically.

Results

Serum malondialdehyde and nitric oxide levels were significantly higher in acute intestinal amebiasis patients than healthy controls (P<0.001).

Conclusions

These results suggest that oxidative and nitrosative stress may play a major role in tissue damage in acute intestinal amebiasis patients. Also these parameters can be used to supplement the conventional microscopic method for reliable diagnosis of intestinal amebiasis.     

Spiral CT Angiography: Applications in Neurovascular Imaging

Background

The advent of Spiral Computed Tomographic (CT) angiography has provided the patients a non-invasive, accurate and fast modality of imaging the vasculature.

Methods

Spiral CT angiography was performed in 30 patients to evaluate intracranial circulation using standard protocols of data acquisition. The images were processed and reconstructed in 3-dimension to delineate anatomy and pathology accurately.

Results

The study established that CT angiography is an accurate modality for evaluating the intracranial circulation in a variety of abnormalities. It is safe both in terms of being non-invasive and exposure to radiation. It has a distinct advantage over other non-invasive modalities of imaging like MRI in the evaluation of patients with metallic stents and clips.

Conclusion

CT angiography has tremendous potential in imaging the intracranial vasculature. It is unquestionably safer than catheter angiography as it avoids arterial puncture and intra-arterial catheter manipulation. It is fast and capable of producing excellent 3-dimensional images of the intracranial vasculature.Key Words: Neurovascular imaging, Spiral CT, CT Angiography     

Evaluation of an Intelligent Tutoring System in Pathology: Effects of External Representation on Performance Gains,Metacognition, and Acceptance

Objective

Determine effects of computer-based tutoring on diagnostic performance gains, meta-cognition, and acceptance using two different problem representations. Describe impact of tutoring on spectrum of diagnostic skills required for task performance. Identify key features of student-tutor interaction contributing to learning gains.

Design

Prospective, between-subjects study, controlled for participant level of training. Resident physicians in two academic pathology programs spent four hours using one of two interfaces which differed mainly in external problem representation. The case-focused representation provided an open-learning environment in which students were free to explore evidence-hypothesis relationships within a case, but could not visualize the entire diagnostic space. The knowledge-focused representation provided an interactive representation of the entire diagnostic space, which more tightly constrained student actions.

Measurements

Metrics included results of pretest, post-test and retention-test for multiple choice and case diagnosis tests, ratios of performance to student reported certainty, results of participant survey, learning curves, and interaction behaviors during tutoring.

Results

Students had highly significant learning gains after one tutoring session. Learning was retained at one week. There were no differences between the two interfaces in learning gains on post-test or retention test. Only students in the knowledge-focused interface exhibited significant metacognitive gains from pretest to post-test and pretest to retention test. Students rated the knowledge-focused interface significantly higher than the case-focused interface.

Conclusions

Cognitive tutoring is associated with improved diagnostic performance in a complex medical domain. The effect is retained at one-week post-training. Knowledge-focused external problem representation shows an advantage over case-focused representation for metacognitive effects and user acceptance.     

Health Professionals Expose TB Patients to Stigmatization in Society: Insights from Communities in an Urban District in Ghana

Objectives

To determine how the activities and attitudes of health professionals expose TB patients to stigmatization in the community.

Design

Qualitative research approach using individual interviews and focus groups

Setting

Shama Ahanta East Metropolitan district in the western region of Ghana

Participants

Members in nine communities in the district

Outcome measures

Words and statements that depict how activities and attitudes of health professionals may expose TB patients to stigmatization

Results

Five interrelated ways by which activities and attitudes of health professionals may expose TB patients to stigmatization in the community were identified in data: TB control practices; fear-based responses to TB; inappropriate health education messages; medical licensing for sellers; and prohibition of burial rites.

Conclusions

The findings may explain the diagnostic delay and low TB case detection rate in Ghana. This calls for intensification of education on TB and regular organization of refresher courses and possibly retraining of health professionals in TB control and management. When health professionals are seen to be treating TB patients as ‘normal’ individuals, it has the potential of changing the society''s perception about the disease.     

Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience

Background

Systematic study of clinical phenotypes is important for a better understanding of the genetic basis of human diseases and more effective gene-based disease management. A key aspect in facilitating such studies requires standardized representation of the phenotype data using common data elements (CDEs) and controlled biomedical vocabularies. In this study, the authors analyzed how a limited subset of phenotypic data is amenable to common definition and standardized collection, as well as how their adoption in large-scale epidemiological and genome-wide studies can significantly facilitate cross-study analysis.

Methods

The authors mapped phenotype data dictionaries from five different eMERGE (Electronic Medical Records and Genomics) Network sites studying multiple diseases such as peripheral arterial disease and type 2 diabetes. For mapping, standardized terminological and metadata repository resources, such as the caDSR (Cancer Data Standards Registry and Repository) and SNOMED CT (Systematized Nomenclature of Medicine), were used. The mapping process comprised both lexical (via searching for relevant pre-coordinated concepts and data elements) and semantic (via post-coordination) techniques. Where feasible, new data elements were curated to enhance the coverage during mapping. A web-based application was also developed to uniformly represent and query the mapped data elements from different eMERGE studies.

Results

Approximately 60% of the target data elements (95 out of 157) could be mapped using simple lexical analysis techniques on pre-coordinated terms and concepts before any additional curation of terminology and metadata resources was initiated by eMERGE investigators. After curation of 54 new caDSR CDEs and nine new NCI thesaurus concepts and using post-coordination, the authors were able to map the remaining 40% of data elements to caDSR and SNOMED CT. A web-based tool was also implemented to assist in semi-automatic mapping of data elements.

Conclusion

This study emphasizes the requirement for standardized representation of clinical research data using existing metadata and terminology resources and provides simple techniques and software for data element mapping using experiences from the eMERGE Network.     

The UMLS-CORE project: a study of the problem list terminologies used in large healthcare institutions

Objective

To study existing problem list terminologies (PLTs), and to identify a subset of concepts based on standard terminologies that occur frequently in problem list data.

Design

Problem list terms and their usage frequencies were collected from large healthcare institutions.

Measurement

The pattern of usage of the terms was analyzed. The local terms were mapped to the Unified Medical Language System (UMLS). Based on the mapped UMLS concepts, the degree of overlap between the PLTs was analyzed.

Results

Six institutions submitted 76 237 terms and their usage frequencies in 14 million patients. The distribution of usage was highly skewed. On average, 21% of unique terms already covered 95% of usage. The most frequently used 14 395 terms, representing the union of terms that covered 95% of usage in each institution, were exhaustively mapped to the UMLS. 13 261 terms were successfully mapped to 6776 UMLS concepts. Less frequently used terms were generally less ‘mappable’ to the UMLS. The mean pairwise overlap of the PLTs was only 21% (median 19%). Concepts that were shared among institutions were used eight times more often than concepts unique to one institution. A SNOMED Problem List Subset of frequently used problem list concepts was identified.

Conclusions

Most of the frequently used problem list terms could be found in standard terminologies. The overlap between existing PLTs was low. The use of the SNOMED Problem List Subset will save developmental effort, reduce variability of PLTs, and enhance interoperability of problem list data.     

Tamoxifen Therapy for Breast Cancer and Endometrial Pathology

Background

Tamoxifen, used as adjuvant therapy for carcinoma breast in postmenopausal women to prevent relapse has estrogenic effect on the endometrium.

Methods

104 patients on tamoxifen for more than six months were subjected to a clinical examination and transvaginal sonography. Patients with endometrial thickness > 8 mm were further evaluated by hysteroscopy and endometrial biopsy.

Results

35(34%) patients were symptomatic. The average endometrial thickness was 11.2 mm which correlated with duration of tamoxifen use. 27(48%) patients had abnormal hysteroscopic findings. 35 (63%) of endometrial biopsies revealed abnormal endometrium. One case of endometrial carcinoma was diagnosed. The results were statistically analysed. There is a significant association between symptomatic status and endometrial thickness and duration of tamoxifen use.

Conclusion

All patients on long term tamoxifen should be annually screened for endometrial pathology.Key Words: Tamoxifen, Endometrium, Transvaginal sonography     

Role of computed tomography before lumbar puncture: a survey of clinical practice

Introduction

It is becoming increasingly common to request computed tomography (CT) to rule out space occupying lesions before lumbar puncture (LP), even in patients with no clinical signs. Imaging trends within a busy district general hospital in Oxfordshire, UK were analysed with results used to clarify when imaging should be considered mandatory.

Method

A retrospective six month sample was obtained comprising all adults considered for LP. Observed frequencies of abnormal examination findings compared with abnormal investigations were used to determine sensitivity, specificity, positive predictive, and negative predictive values to assess the validity of using a normal clinical examination as a basis for excluding CT.

Results

64 patients were considered for LP. In total, 58 patients underwent LP, with a single patient receiving two. After an abnormal CT scan, six patients did not undergo a planned LP. In all six of these cases subarachnoid haemorrhage was detected, and in all cases this was considered a probable diagnosis. In no case was an LP precluded by an unsuspected space occupying lesion. Neurological examination showed a sensitivity of 0.72 (0.52 to 0.93), specificity 0.78 (0.64 to 0.91), positive predictive value 0.61 (0.41 to 0.83), and negative predictive value 0.85 (0.73 to 0.97).

Discussion

The high sensitivity and negative predictive values support normal neurological examination as an effective predictor of normal CT scan. This permits the recommendation in cases where subarachnoid haemorrhage is not suspected, a CT scan can be avoided provided there are no abnormal findings on physical or fundoscopic examination.     

Research and applications: MilxXplore: a web-based system to explore large imaging datasets

Objective

As large-scale medical imaging studies are becoming more common, there is an increasing reliance on automated software to extract quantitative information from these images. As the size of the cohorts keeps increasing with large studies, there is a also a need for tools that allow results from automated image processing and analysis to be presented in a way that enables fast and efficient quality checking, tagging and reporting on cases in which automatic processing failed or was problematic.

Materials and methods

MilxXplore is an open source visualization platform, which provides an interface to navigate and explore imaging data in a web browser, giving the end user the opportunity to perform quality control and reporting in a user friendly, collaborative and efficient way.

Discussion

Compared to existing software solutions that often provide an overview of the results at the subject''s level, MilxXplore pools the results of individual subjects and time points together, allowing easy and efficient navigation and browsing through the different acquisitions of a subject over time, and comparing the results against the rest of the population.

Conclusions

MilxXplore is fast, flexible and allows remote quality checks of processed imaging data, facilitating data sharing and collaboration across multiple locations, and can be easily integrated into a cloud computing pipeline. With the growing trend of open data and open science, such a tool will become increasingly important to share and publish results of imaging analysis.     

Three Dimensional Spiral CT Imaging of the Musculoskeletal System: Application and Advantages

Background

Clinical applications of spiral computed tomography (CT) have increased extensively over the past decade and continue to widen rapidly. The introduction of three-dimensional(3-D) reconstruction in CT technology has revolutionized medical imaging. This advancement has been possible due to the combination of spiral computed tomography and various 3-D reconstruction protocols which have permitted rapid and comprehensive examination of all regions of the body. It has unequivocal advantages in the preoperative planning of craniofacial surgery, assessment of complex fractures of the skeletal system especially pelvis and in the surgical treatment of dysplastic hips in children.

Methods

3-D spiral CT imaging of various parts of the musculoskeletal system was carried out in 60 cases using available protocols, at the CT scan center of a large tertiary care service hospital.

Results

The study provided a new approach in the analysis of complex anatomic relationships of the musculoskeletal system. Therapeutic planning whether surgical or medical was to a great extent aided by the anatomic information available from these images.

Conclusion

3-D CT imaging is a rapid, non-invasive and accurate technique for diagnosis, pre-operative evaluation as well as post-operative assessment of a large number of musculoskeletal diseases. 3-D CT studies have come to stay and with continued improvement in CT technology it has now become an integral part of imaging studies of the musculoskeletal system.Key Words: Spiral CT, 3-dimensional imaging, Musculoskeletal system     

Facilitating Clinical Outcomes Assessment through the Automated Identification of Quality Measures for Prostate Cancer Surgery

Objectives

The College of American Pathologists (CAP) Category 1 quality measures, tumor stage, Gleason score, and surgical margin status, are used by physicians and cancer registrars to categorize patients into groups for clinical trials and treatment planning. This study was conducted to evaluate the effectiveness of an application designed to automatically extract these quality measures from the postoperative pathology reports of patients having undergone prostatectomies for treatment of prostate cancer.

Design

An application was developed with the Clinical Outcomes Assessment Toolkit that uses an information pipeline of regular expressions and support vector machines to extract CAP Category 1 quality measures. System performance was evaluated against a gold standard of 676 pathology reports from the University of California at Los Angeles Medical Center and Brigham and Women''s Hospital. To evaluate the feasibility of clinical implementation, all pathology reports were gathered using administrative codes with no manual preprocessing of the data performed.

Measurements

The sensitivity, specificity, and overall accuracy of system performance were measured for all three quality measures. Performance at both hospitals was compared, and a detailed failure analysis was conducted to identify errors caused by poor data quality versus system shortcomings.

Results

Accuracies for Gleason score were 99.7%, tumor stage 99.1%, and margin status 97.2%, for an overall accuracy of 98.67%. System performance on data from both hospitals was comparable. Poor clinical data quality led to a decrease in overall accuracy of only 0.3% but accounted for 25.9% of the total errors.

Conclusion

Despite differences in document format and pathologists'' reporting styles, strong system performance indicates the potential of using a combination of regular expressions and support vector machines to automatically extract CAP Category 1 quality measures from postoperative prostate cancer pathology reports.