A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies.
A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies.
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DOI：
10.1186/1472-6947-3-6
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发表时间：
2003-06-16
影响因子：
3.5
通讯作者：
Berman, Jules J
中科院分区：
文献类型：
--
作者：
Berman, Jules J
背景：大型生物医学数据集已成为医学研究人员越来越重要的资源。现代生物医学数据集使用标准术语进行注释，以描述数据并支持数据库之间的数据链接。最大的生物医学术语列表是国家医学图书馆的统一医学语言系统（UMLS）。UMLS包含从近100个医学词汇表中收集的200多万个生物医学术语。UMLS中包含的许多词汇表在使用上都有限制，这使得共享或分发UMLS注释的研究数据变得不可能。然而，一个子集的UMLS词汇表，指定类别0的UMLS，可以用来注释和共享数据集，而不违反UMLS License Agreement.METHODS：UMLS类别0词汇表可以提取从父UMLS元词库使用Perl脚本提供了这篇文章。有43个0类词汇表可以自由地用于研究目的，而不违反UMLS许可协议。0类词汇表包括：MESH（医学主题词）、NCBI（国家生物信息学中心）分类和ICD-9-CM（国际疾病分类-9-临床修饰语）。结果：包含所有0类术语和概念的提取文件长度为72，581，138字节，包含1，029，161个术语。UMLS Metathesaurus MRCON文件（2003年1月）的长度为151，048，493字节，包含2，146，899个术语。因此，0类词汇表的总规模大约是UMLS元词库的一半。使用完整的UMLS元词库和0类词汇表自动编码了567，921个不同医学短语的大型公开可用列表。有545,321个短语与UMLS术语有一个或多个匹配，而468,785个短语与0类术语有一个或多个匹配。这表明，当两个词汇进行评估，他们的健身找到至少一个术语的医疗短语，0类词汇执行86%，以及完整的UMLS元词库。结论：0类词汇的UMLS构成一个大的命名，可用于生物医学研究人员注释生物医学数据。这些带注释的数据集可以在不违反UMLS许可协议的情况下用于研究目的。这些词汇表对于共享来自不同生物医学数据集的异构数据可能特别重要。提取0类词汇表的软件工具是免费提供的Perl脚本，这些脚本已进入公共领域，并随本文一起分发。
BACKGROUND: Large biomedical data sets have become increasingly important resources for medical researchers. Modern biomedical data sets are annotated with standard terms to describe the data and to support data linking between databases. The largest curated listing of biomedical terms is the the National Library of Medicine's Unified Medical Language System (UMLS). The UMLS contains more than 2 million biomedical terms collected from nearly 100 medical vocabularies. Many of the vocabularies contained in the UMLS carry restrictions on their use, making it impossible to share or distribute UMLS-annotated research data. However, a subset of the UMLS vocabularies, designated Category 0 by UMLS, can be used to annotate and share data sets without violating the UMLS License Agreement.METHODS: The UMLS Category 0 vocabularies can be extracted from the parent UMLS metathesaurus using a Perl script supplied with this article. There are 43 Category 0 vocabularies that can be used freely for research purposes without violating the UMLS License Agreement. Among the Category 0 vocabularies are: MESH (Medical Subject Headings), NCBI (National Center for Bioinformatics) Taxonomy and ICD-9-CM (International Classification of Diseases-9-Clinical Modifiers).RESULTS: The extraction file containing all Category 0 terms and concepts is 72,581,138 bytes in length and contains 1,029,161 terms. The UMLS Metathesaurus MRCON file (January, 2003) is 151,048,493 bytes in length and contains 2,146,899 terms. Therefore the Category 0 vocabularies, in aggregate, are about half the size of the UMLS metathesaurus.A large publicly available listing of 567,921 different medical phrases were automatically coded using the full UMLS metatathesaurus and the Category 0 vocabularies. There were 545,321 phrases with one or more matches against UMLS terms while 468,785 phrases had one or more matches against the Category 0 terms. This indicates that when the two vocabularies are evaluated by their fitness to find at least one term for a medical phrase, the Category 0 vocabularies performed 86% as well as the complete UMLS metathesaurus.CONCLUSION: The Category 0 vocabularies of UMLS constitute a large nomenclature that can be used by biomedical researchers to annotate biomedical data. These annotated data sets can be distributed for research purposes without violating the UMLS License Agreement. These vocabularies may be of particular importance for sharing heterogeneous data from diverse biomedical data sets. The software tools to extract the Category 0 vocabularies are freely available Perl scripts entered into the public domain and distributed with this article.