The Semantic Web As "Perfection Seeking:" A View from Drug Terminology (original) (raw)
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Journal of Biomedical Informatics, 2009
The Medical Entities Dictionary (MED) has served as a unified terminology at New York Presbyterian Hospital and Columbia University for more than 20 years. It was initially created to allow the clinical data from the disparate information systems (e.g., radiology, pharmacy, and multiple laboratories, etc.) to be uniquely codified for storage in a single data repository, and functions as a real time terminology server for clinical applications and decision support tools. Being conceived as a knowledge base, the MED incorporates relationships among local terms, between local terms and external standards, and additional knowledge about terms in a semantic network structure. Over the past two decades, we have sought to develop methods to maintain, audit and improve the content of the MED, such that it remains true to its original design goals. This has resulted in a complex, multi-faceted process, with both manual and automated components. In this paper, we describe this process, with examples of its effectiveness. We believe that our process provides lessons for others who seek to maintain complex, concept-oriented controlled terminologies.
An Ontology Change Management System: An experiment on a health care case study
2nd International Conference on Knowledge Engineering and Ontology Developement (KEOD’10), Valencia, Spain, 2010
Numerous ontologies have been developed for life science domains. These ontologies are continuously changing. Thus, it is becoming important to study and to manage these changes in order to keep all dependent ontologies and their related mappings consistent. The aim of this paper is to propose an agent based approach enabling not only ontology and ontology mapping evolution analysis but also to manage their changes. An experiment in health care illustrates the benefits of our approach. We apply our algorithm and implementation prototype p 2 OEManager to eye specialist ontology (ESO) and primary health care ontology (PCO), and particularly, we use the prototype and our ontology agent model to manage some significant changes in the ESO ontology.
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Lecture Notes in Computer Science, 2013
Understanding ontology evolution is becoming an active topic of interest to ontology engineers, e.g., we have large collaborative developed ontologies but, unlike software engineering, comparatively little is understood about the dynamics of historical changes, especially at a fine level of granularity. Only recently has there been a systematic analysis of changes across ontology versions, but still at a coarse-grained level. The National Cancer Institute (NCI) Thesaurus (NCIt) is a large, collaboratively-developed ontology, used for various Web and research-related purposes, e.g., as a medical research controlled vocabulary. The NCI has published ten years worth of monthly versions of the NCIt as Web Ontology Language (OWL) documents, and has also published reports on the content of, development methodology for, and applications of the NCIt. In this paper, we carry out a fine-grained analysis of the asserted axiom dynamics throughout the evolution of the NCIt from 2003 to 2012. From this, we are able to identify axiomatic editing patterns that suggest significant regression editing events in the development history of the NCIt.
A bottom-up approach to creating an ontology for medication indications
Journal of the American Medical Informatics Association, 2021
Objectives The study sought to learn if it were possible to develop an ontology that would allow the Food and Drug Administration approved indications to be expressed in a manner computable and comparable to what is expressed in an electronic health record. Materials and Methods A random sample of 1177 of the 3000+ extant, distinct medical products (identified by unique new drug application numbers) was selected for investigation. Close manual examination of the indication portion of the labels for these drugs led to the development of a formal model of indications. Results The model represents each narrative indication as a disjunct of conjuncts of assertions about an individual. A desirable attribute is that each assertion about an individual should be testable without reference to other contextual information about the situation. The logical primitives are chosen from 2 categories (context and conditions) and are linked to an enumeration of uses, such as prevention. We found that...
Definitions management: A semantics-based approach for clinical documentation in healthcare delivery
2005
Structured Clinical Documentation is a fundamental component of the healthcare enterprise, linking both clinical (e.g., electronic health record, clinical decision support) and administrative functions (e.g., evaluation and management coding, billing). Documentation templates have proven to be an effective mechanism for implementing structured clinical documentation. The ability to create and manage definitions, i.e., definitions management, for various concepts such as diseases, drugs, contraindications, complications, etc. is crucial for creating and maintaining documentation templates in a consistent and cohesive manner across the organization. Definitions management involves the creation and management of concepts that may be a part of controlled vocabularies, domain models and ontologies. In this paper, we present a realworld implementation of a semantics-based approach to automate structured clinical documentation based on a description logics (DL) system for ontology management. In this context we will introduce the ontological underpinnings on which clinical documents are based, namely the domain, document and presentation ontologies. We will present techniques that leverage these ontologies to render static and dynamic templates that contain branching logic. We will also evaluate the role of these ontologies in the context of managing the impact of definition changes on the creation and rendering of these documentation templates, and the ability to retrieve documentation templates and their instances precisely in a given clinical context.
Representation of change in controlled medical terminologies
Artificial Intelligence in Medicine, 1999
Computer-based systems that support health care require large controlled terminologies to manage names and meanings of data elements. These terminologies are not static, because change in health care is inevitable. To share data and applications in health care, we need standards not only for terminologies and concept representation, but also for representing change. To develop a principled approach to managing change, we analyze the requirements of controlled medical terminologies and consider features that frame knowledgerepresentation systems have to offer. Based on our analysis, we present a concept model, a set of change operations, and a change-documentation model that may be appropriate for controlled terminologies in health care. We are implementing our framework in a system that addresses the problem of terminology divergence due to local adaptations.
Studies in Health Technology and Informatics
This paper describes the development and evaluation of a Canadian drug ontology (OCRx), built to provide a normalized and standardized description of drugs that are authorized to be marketed in Canada. OCRx aims to improve the usability and interoperability of drugs terminologies for a non-ambiguous access to drugs information that is available in electronic health record systems. We present the first release of OCRx that is described in Web Ontology Language and aligned to the Identification of Medicinal Product (IDMP) standards. For comparison purposes, OCRx is mapped to RxNorm, its US variant.
Finding and Characterizing Changes in Ontologies
Lecture Notes in Computer Science, 2002
Recently, the interest in the use of ontologies -which can be seen as formal representations of conceptual models -has increased because of the excitement about the vision of a "Semantic Web". When ontologies are used on the web, the distributed and dynamic nature of it requires advanced support for change management. This paper discusses the working of OntoView, a web-based change management system for ontologies. OntoView provides a transparent interface to different versions of ontologies, by maintaining not only the transformations between them, but also the conceptual relation between concepts in different versions. It uses several rules to find changes in ontologies and it visualizes them -and some of their possible consequences -in the file representations. The user is able to specify the conceptual implication of the differences, which allows the interoperability of data that is described by the ontologies. This paper briefly describes the system and presents the mechanism that we used to find and classify changes in RDFS / DAML ontologies. It also shows how users can specify the conceptual implication of changes to help interoperability.
Supporting Evolving Ontologies on the Internet
Lecture Notes in Computer Science, 2002
The idea of a "Semantic Web" has created a lot of interest in the use of ontologies-formal descriptions of a part of the world-for describing the meaning of information on the web. However, when ontologies are used on the web, several problems appear: how can different ontologies be combined, what happens when they are changed, and how should they be adapted for new tasks. Those questions require the management of ontologies, their use and their evolution. This paper describes a research project that will investigate the management of ontologies in an web-based setting.