scholarly journals Mapping the Gene Ontology Into the Unified Medical Language System

2004 ◽  
Vol 5 (4) ◽  
pp. 354-361 ◽  
Author(s):  
Jane Lomax ◽  
Alexa T. McCray
Keyword(s):  
Gene Ontology ◽  
Clinical Medicine ◽  
Gene Products ◽  
National Library ◽  
Web Based ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language ◽  
Large Numbers ◽  
Go Terms

We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics.

scholarly journals A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System

2020 ◽  
Vol 27 (10) ◽  
pp. 1568-1575 ◽  
Author(s):  
Fengbo Zheng ◽  
Jay Shi ◽  
Yuntao Yang ◽  
W Jim Zheng ◽  
Licong Cui
Keyword(s):  
Gene Ontology ◽  
Information Systems ◽  
Random Sample ◽  
English Language ◽  
Snomed Ct ◽  
Domain Experts ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language ◽  
Original Concept

Abstract Objective The Unified Medical Language System (UMLS) integrates various source terminologies to support interoperability between biomedical information systems. In this article, we introduce a novel transformation-based auditing method that leverages the UMLS knowledge to systematically identify missing hierarchical IS-A relations in the source terminologies. Materials and Methods Given a concept name in the UMLS, we first identify its base and secondary noun chunks. For each identified noun chunk, we generate replacement candidates that are more general than the noun chunk. Then, we replace the noun chunks with their replacement candidates to generate new potential concept names that may serve as supertypes of the original concept. If a newly generated name is an existing concept name in the same source terminology with the original concept, then a potentially missing IS-A relation between the original and the new concept is identified. Results Applying our transformation-based method to English-language concept names in the UMLS (2019AB release), a total of 39 359 potentially missing IS-A relations were detected in 13 source terminologies. Domain experts evaluated a random sample of 200 potentially missing IS-A relations identified in the SNOMED CT (U.S. edition) and 100 in Gene Ontology. A total of 173 of 200 and 63 of 100 potentially missing IS-A relations were confirmed by domain experts, indicating that our method achieved a precision of 86.5% and 63% for the SNOMED CT and Gene Ontology, respectively. Conclusions Our results showed that our transformation-based method is effective in identifying missing IS-A relations in the UMLS source terminologies.

Navigating to Knowledge

1995 ◽  
Vol 34 (01/02) ◽  
pp. 214-231 ◽  
Author(s):  
M. S. Tuttle ◽  
W. G. Cole ◽  
D. D. Sherertz ◽  
S. J. Nelson
Keyword(s):  
National Cancer Institute ◽  
Point Of Care ◽  
Visual Representation ◽  
Medical Knowledge ◽  
National Library ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language ◽  
Computer Based ◽  
The U.S

Abstract:One way to fulfill point-of-care knowledge needs is to present caregivers with a visual representation of the available “answers”. Using such a representation, caregivers can recognize what they want, rather than have to recall what they need, and then navigate to an appropriate answer. Given selected pieces of information from a computer-based patient record, an interface can anticipate certain knowledge needs by initializing caregiver navigation in a semantic neighborhood of answers likely to be relevant to the patient at hand. These notions draw heavily on two collaborative projects – the U.S. National Library of Medicine Unified Medical Language System® and the U.S. National Cancer Institute Knowledge Server. Both of these projects support navigation because they make the structure of medical knowledge explicit in a way that can be exploited by human interfaces.

scholarly journals The Unified Medical Language System SPECIALIST Lexicon and Lexical Tools: Development and applications

2020 ◽  
Vol 27 (10) ◽  
pp. 1600-1605 ◽  
Author(s):  
Chris J Lu ◽  
Amanda Payne ◽  
James G Mork
Keyword(s):  
Concept Mapping ◽  
Language Processing ◽  
Vital Role ◽  
Unstructured Data ◽  
National Library ◽  
Language System ◽  
Unified Medical Language System ◽  
The Core ◽  
Medical Language ◽  
Recent Developments

Abstract Natural language processing (NLP) plays a vital role in modern medical informatics. It converts narrative text or unstructured data into knowledge by analyzing and extracting concepts. A comprehensive lexical system is the foundation to the success of NLP applications and an essential component at the beginning of the NLP pipeline. The SPECIALIST Lexicon and Lexical Tools, distributed by the National Library of Medicine as one of the Unified Medical Language System Knowledge Sources, provides an underlying resource for many NLP applications. This article reports recent developments of 3 key components in the Lexicon. The core NLP operation of Unified Medical Language System concept mapping is used to illustrate the importance of these developments. Our objective is to provide generic, broad coverage and a robust lexical system for NLP applications. A novel multiword approach and other planned developments are proposed.

scholarly journals Towards a Semantic Lexicon for Biological Language Processing

2005 ◽  
Vol 6 (1-2) ◽  
pp. 61-66 ◽  
Author(s):  
Karin Verspoor
Keyword(s):  
Molecular Biology ◽  
Language Processing ◽  
Semantic Information ◽  
Text Processing ◽  
National Library ◽  
Important Resource ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language

This paper explores the use of the resources in the National Library of Medicine's Unified Medical Language System (UMLS) for the construction of a lexicon useful for processing texts in the field of molecular biology. A lexicon is constructed from overlapping terms in the UMLS SPECIALIST lexicon and the UMLS Metathesaurus to obtain both morphosyntactic and semantic information for terms, and the coverage of a domain corpus is assessed. Over 77% of tokens in the domain corpus are found in the constructed lexicon, validating the lexicon's coverage of the most frequent terms in the domain and indicating that the constructed lexicon is potentially an important resource for biological text processing.

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