Evaluation of the Unified Medical Language System as a Medical Knowledge Source

Bodenreider, Olivier; Burgun, Anita; Botti, G.; Fieschi, Marius; Beux, P. Le; Kohler, François

doi:10.1136/jamia.1998.0050076

Cited by 28 publications

(15 citation statements)

References 12 publications

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“…Such database‐specific additions also explain some false‐negative codes without siblings in the reference set. Inconsistencies in the Metathesaurus such as missing identification of equivalent codes and incomplete coverage of vocabularies have been discussed before …”

Section: Discussionmentioning

confidence: 99%

“…Such database-specific additions also explain some false-negative codes without siblings in the reference set. Inconsistencies in the Metathesaurus such as missing identification of equivalent codes and incomplete coverage of vocabularies have been discussed before [28][29][30][31]. The SAFEGUARD reference set contained only codes for diagnoses but no codes for laboratory, imaging or ECG results.…”

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confidence: 99%

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CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project

Becker

Avillach

Romio

et al. 2017

Pharmacoepidemiology and Drug

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BackgroundAssessment of drug and vaccine effects by combining information from different healthcare databases in the European Union requires extensive efforts in the harmonization of codes as different vocabularies are being used across countries. In this paper, we present a web application called CodeMapper, which assists in the mapping of case definitions to codes from different vocabularies, while keeping a transparent record of the complete mapping process.MethodsCodeMapper builds upon coding vocabularies contained in the Metathesaurus of the Unified Medical Language System. The mapping approach consists of three phases. First, medical concepts are automatically identified in a free‐text case definition. Second, the user revises the set of medical concepts by adding or removing concepts, or expanding them to related concepts that are more general or more specific. Finally, the selected concepts are projected to codes from the targeted coding vocabularies. We evaluated the application by comparing codes that were automatically generated from case definitions by applying CodeMapper's concept identification and successive concept expansion, with reference codes that were manually created in a previous epidemiological study.ResultsAutomated concept identification alone had a sensitivity of 0.246 and positive predictive value (PPV) of 0.420 for reproducing the reference codes. Three successive steps of concept expansion increased sensitivity to 0.953 and PPV to 0.616.ConclusionsAutomatic concept identification in the case definition alone was insufficient to reproduce the reference codes, but CodeMapper's operations for concept expansion provide an effective, efficient, and transparent way for reproducing the reference codes.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project

Becker

Avillach

Romio

et al. 2017

Pharmacoepidemiology and Drug

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“…We hope that the efforts of ODS to create and support USA data standards for dietary supplements continue, and we hope that emerging standards across the Atlantic address the same requirements that motivated our solution. The National Library of Medicine's UMLS System [40][41][42] is a source of linking multiple (over 100) standard healthcare standard vocabularies and could be tool to link RxNorm to SNOMED CT or other classifications that emerge as standards in this area.…”

Section: Discussionmentioning

confidence: 99%

Trans-Atlantic data harmonization in the classification of medicines and dietary supplements: A challenge for epidemiologic study and clinical research

Moyers

Richesson

Krischer

2008

International Journal of Medical Informatics

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Objectives-As international scientific collaboration increases, there is a growing requirement for research data to be comparable among countries. Despite the importance of medication and dietary supplement data in research, there are no international standards for the collection and storage of these data. In the absence of such standards, we needed to adopt a strategy for classification and coding of medications and dietary supplements to meet demands of our multi-national study.Methods-Given the inter-country variations in nomenclature that characterize prescription, overthe-counter (OTC) medications, traditional herbal medicines, and dietary supplements, we adopted RxNorm as a data standard for medication data, and developed an independent system that extends this standard and allows for flexible and scalable data collection for dietary supplements.Results-RxNorm was implemented in May 2005 and as of July 2006, coverage has been 99%, at the level of active ingredients, of all the medications reported in our study. Development of a dietary supplement database began in August 2005, and has thus far coded some 1200 dietary supplements and 650 infant formula products and forms from the four countries in our study. Conclusion-The methods we have used to collect, store, and manage medication and dietary supplement data serve as interim solutions until international standards are developed. It is hoped that such standards will ultimately emerge, and that our strategy and data model will be of value in other research environments in the immediate future. Keywords medications; dietary supplements; data standardization; data management; epidemiological methods; clinical research Brief AccountWhat was known before the study?• Epidemiologic and other human research studies collect data on the use of pharmaceutical products and dietary supplements.• There is no standard international or global coding or classification scheme for these data.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptInt J Med Inform. Author manuscript; available in PMC 2009 January 1. Published in final edited form as:Int J Med Inform. 2008 January ; 77(1): 58-67. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript• There is no standard practice for collecting and storing these data, nor is there a standard data model to guide local efforts.What this study has added to the body of knowledge?• This work reviews current data standards and "best" practices (both in the USA and the EU) for the collection and storage of data related to the use of pharm...

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“…Also this information can be used for subsequent filtering and ranking we decided to include all available associations for the integration step. We then used the UMLS Metathesaurus [44] to derive mappings between the different medical vocabularies and integrate the different gene-disease association resources which had used different disease vocabularies. The set of gene-disease associations used for analysis therefore represents the non-redundant sum of all individual integrated sources.…”

Section: Methodsmentioning

confidence: 99%

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration

et al. 2016

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BackgroundDeep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations have generated high-resolution molecular maps of putative relevance for understanding disease initiation and progression. Yet, it is unclear how to advance an observation of comorbidity relations (one disease to others) to a molecular understanding of the driver processes and associated biomarkers.ResultsSince Chronic Obstructive Pulmonary disease (COPD) has emerged as a central hub in temporal comorbidity networks, we developed a systematic integrative data-driven framework to identify shared disease-associated genes and pathways, as a proxy for the underlying generative mechanisms inducing comorbidity. We integrated records from approximately 13 M patients from the Medicare database with disease-gene maps that we derived from several resources including a semantic-derived knowledge-base. Using rank-based statistics we not only recovered known comorbidities but also discovered a novel association between COPD and digestive diseases. Furthermore, our analysis provides the first set of COPD co-morbidity candidate biomarkers, including IL15, TNF and JUP, and characterizes their association to aging and life-style conditions, such as smoking and physical activity.ConclusionsThe developed framework provides novel insights in COPD and especially COPD co-morbidity associated mechanisms. The methodology could be used to discover and decipher the molecular underpinning of other comorbidity relationships and furthermore, allow the identification of candidate co-morbidity biomarkers.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1291-3) contains supplementary material, which is available to authorized users.

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Evaluation of the Unified Medical Language System as a Medical Knowledge Source

Abstract: After UMLS was used for five years as a knowledge source for representing 1500 complex medical procedures in MAOUSSC, its value is considered significant. Future editions of the UMLS are expected to improve representation of inter-concept relationships and global consistency.

Cited by 28 publications

References 12 publications

CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project

CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project

Trans-Atlantic data harmonization in the classification of medicines and dietary supplements: A challenge for epidemiologic study and clinical research

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration

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