Clinical and Biomolecular Ontologies for E-Health

Clinical and Biomolecular Ontologies for E-Health

Mario Ceresa (Politecnico di Milano, Italy)
DOI: 10.4018/978-1-60566-002-8.ch011
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Abstract

This chapter mainly focuses on biomedical knowledge representation and its use in biomedicine. It first illustrates the existent more relevant bioinformatics resources and why they need to be better integrated. Then it describes what the main problems that machines can encounter in processing the factual biomedical knowledge are, what terminologies, classifications and ontologies are, and why they could help in better organizing and exploiting the bioinformatics resources available online. The authors hope that a concise perspective of the field and a list of selected resources, commented with their scope and usability, may help interested people in quickly understanding the main principles of knowledge representation in biomedicine and its high relevance for modern biomedical research and e-health.

Key Terms in this Chapter

Terminology: A collection of names of the entities involved in a domain. It simply states which are the principal terms used in the domain without any further information. Though it is a quite simplistic approach, yet it is extremely useful because helps computer programs to recognize the relevant terms and concentrate only on them. Although sometimes could be difficult to understand the difference between a terminology and a controlled vocabulary, the former is just a list of the terms used in a domain, while the latter guarantees that its terms are precise, accurate and unequivocal.

Biomedical Informatics: The discipline that studies biomedical information and knowledge, focusing in particular on their structure, acquisition, integration, management, and optimal use. It adopts and applies results from a variety of other disciplines including Information Science, Computer Science, Cognitive Science, Statistics and Biometrics, Mathematics, Artificial Intelligence, Operations Research, and basic and clinical Health Sciences.

Proteomics: The study of the whole of all possible proteins (amino acid sequences) of an organism, translated from different transcripts (mRNA sequences transcripted from a nucleotide sequence).

Biomolecular or Genomic Databank: A structured repository of biomolecular, genomic or proteomic data, often integrated with their related biological, medical, clinical, or experimental information. Generally it also provides interfaces and tools for browsing, querying, and sometime analyzing the data it contains.

Genomics: The systematic identification and study of Genomes, each of them including all the whole genetic material of a living organism.

Bioinformatics: A join branch of biology and informatics concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. It comprehends all computational methods and theories applicable to molecular biology and the computer-based techniques for solving biological problems, including manipulation of models and datasets.

Classificat ion: A collection of terms organized in categories. Thus, it includes only the is-a relationship between terms. This enables machines to group together bottom level terms up to their higher level ancestor, e.g. grouping all “lipidic methabolism” related terms under the upper term “metabolism.”

Semantic Network: A graph structure useful to represent the knowledge of a domain. It is composed of a set of objects, the graph nodes, which represent the concepts of the domain, and relations among such objects, the graph arches, which represent the domain knowledge. The semantic networks are also a reasoning tool as it is possible to find relations among the concepts of a semantic network that do not have a direct relation among them. To this aim, it is enough “to follow the arrows” of the network arches that exit from the considered nodes and find in which node the paths meet.

Controlled vocabulary: A collection of precise and universally understandable terms that define and identify the concepts of a domain in a unique and unequivocal way, e.g. the anatomical terminology. Such a vocabulary is said controlled because it is defined and maintained updated by people, the curators, who are expert of the domain the vocabulary refers to. Controlled vocabularies are very useful in extended and complex domains, such as Medicine and Biology, where distinct concepts must be identified with high precision in order to codify, analyze, and communicate the domain knowledge. Though they are similar to terminologies, the difference is that a terminology does not guarantee that its terms are precise, accurate and unequivocal, but it is rather a list of used terms for a specific domain.

Ontology: A semantic structure useful to standardize and provide rigorous definitions of the terminology used in a domain and to describe the knowledge of the domain. It is composed of a controlled vocabulary, which describes the concepts of the considered domain, and a semantic network, which describes the relations among such concepts. Each concept is connected to other concepts of the domain through semantic relations that specify the knowledge of the domain. A general concept can be described by several terms that can be synonyms or characteristic of different domains in which the concept exists. For this reason the ontologies tend to have a hierarchical structure, with generic concepts/terms at the higher levels of the hierarchy and specific concepts/terms at the lover levels, connected by different types of relations.

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Table of Contents
Preface
Athina A. Lazakidou
Acknowledgment
Athina A. Lazakidou
Chapter 1
Sanjay P. Sood, Sandhya Keeroo, Victor W.A. Mbarika, Nupur Prakash, Ankur Seth
It is claimed that seeds of ‘medical informatics’ were sown in 1960s.From this time until the 1990s experts have described the discipline as... Sample PDF
Medical Informatics: Thirty Six Peer-Reviewed Shades
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Chapter 2
D. John Doyle
E-health technology has started to become commonplace in the clinical world, with practitioners setting up their own Web sites to disseminate... Sample PDF
Medical Privacy and the Internet
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Chapter 3
Ana Ferreira, Ricardo Cruz-Correia, Luís Antunes, David Chadwick
This chapter reports the authors’ experiences regarding security of the electronic medical record (EMR). Although the EMR objectives are to support... Sample PDF
Security of Electronic Medical Records
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Chapter 4
György Surján
This chapter outlines the history of medical classifications in a general cultural context. Classification is a general phenomenon in science and... Sample PDF
The Cultural History of Medical Classifications
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Chapter 5
Spyros Kitsiou
A fundamental requirement for achieving continuity of care is commonly accepted to be the integration and interoperability of different clinical... Sample PDF
Overview and Analysis of Electronic Health Record Standards
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Chapter 6
Graham D. Bodie, Mohan J. Dutta, Ambar Basu
This chapter overviews an integrative model of e-health use that connects social disparities at the population level with individual characteristics... Sample PDF
The Integrative Model of E-Health Use
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Chapter 7
Firat Kart
In this chapter we describe a distributed e-healthcare system that uses service oriented architecture as a basis for designing, implementing... Sample PDF
A Distributed E-Healthcare System
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Chapter 8
Davor Mucic
In this chapter the author gives the short review over wide range of telepsychiatry applications. Furthermore, describes completely new and... Sample PDF
Telepsychiatry Within European E-Health
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Chapter 9
Azizah Omar
In this chapter the author discusses several marketing principles and issues related to pitfalls and successes of Telehealth application in the case... Sample PDF
Pitfalls and Successes of a Web-Based Wellness Program
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Chapter 10
Isabel de la Torre Díez
This chapter describes a Web -based application to store and exchange Electronic Health Records (EHR) and medical images in Ophthalmology... Sample PDF
A Web-Based Application to Exchange Electronic Health Records and Medical Images in Ophthalmology
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Chapter 11
Mario Ceresa
This chapter mainly focuses on biomedical knowledge representation and its use in biomedicine. It first illustrates the existent more relevant... Sample PDF
Clinical and Biomolecular Ontologies for E-Health
$37.50
Chapter 12
Roger Tait, Gerald Schaefer
The registration of corresponding patient volumes is often a pre-requisite for medical imaging tasks. Accurate alignment, however, usually results... Sample PDF
Distributed Medical Volume Registration
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Chapter 13
Bill Ag. Drougas
Internet today is one of the most useful tools for information, education and business or entertainment. It is one of the modern technology tools... Sample PDF
Electronic Commerce for Health Products Services-Problems- Quality and Future
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Chapter 14
Christos Bountis
This chapter introduces and reviews the concept of distributed knowledge management within the Healthcare environment and between Healthcare and... Sample PDF
Distributed Knowledge Management in Healthcare
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Chapter 15
Jelena Vucetic
This paper describes business and technological challenges and solutions for a successful emergency telemedicine venture called MediComm. Its... Sample PDF
An Analysis of a Successful Emergency Telemedicine Venture
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Chapter 16
Tammara Massey, Foad Dabiri, Roozbeh Jafari, Hyduke Noshadi, Philip Brisk, Majid Sarrafzadeh
This chapter introduces reconfigurable design techniques for light-weight medical systems. The research presented in this chapter demonstrates how... Sample PDF
Reconfigurable Embedded Medical Systems
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Chapter 17
Konstantinos Perakis
The evolutions in the field of telecommunications technologies, with the robustness and the fidelity these new systems provide, have significantly... Sample PDF
Third Generation (3G) Cellular Networks in Telemedicine: Technological Overview, Applications, and Limitations
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Chapter 18
Anton V. Vladzymyrskyy
This chapter introduces usage of telemedicine consultations in daily clinical practice. Author has describe process of teleconsultation, sample... Sample PDF
Telemedicine Consultations in Daily Clinical Practice: Systems, Organisation, Efficiency
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Chapter 19
Cheon-Pyo Lee, J. P. Shim
Ubiquitous healthcare has become possible with rapid advances in information and communication technologies. Ubiquitous healthcare will bring about... Sample PDF
Ubiquitous Healthcare: Radio Frequency Identification (RFID) in Hospitals
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Chapter 20
Rafael Capilla, Alfonso del Río, Miguel Ángel Valero, José Antonio Sánchez
This chapter deals with the conceptualization, design and implementation of an m-health solution to support ubiquitous, integrated and continuous... Sample PDF
Agile Patient Care with Distributed M-Health Applications
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Chapter 21
Žilbert Tafa
This chapter describes the very actual issues on mobile health (M-H) and home care (H-C) telecare systems, reviewing state of the art as well as... Sample PDF
Mobile Health Applications and New Home Care Telecare Systems: Critical Engineering Issues
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Chapter 22
José Antonio Seoane Fernández, Juan Luis Pérez Ordóñez, Noha Veiguela Blanco
This chapter presents an architecture for the integration of various algorithms for digital image processing (DIP) into web-based information... Sample PDF
A New System for the Integration of Medical Imaging Processing Algorithms into a Web Environment
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Chapter 23
Daniel Welfer
This chapter discusses the concept of open-source picture archiving and communication systems (i.e. PACS), which are low cost, and easy to... Sample PDF
PACS Based on Open-Source Software Components
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Chapter 24
Carolin Kaiser
This chapter introduces a case based reasoning (CBR) system for customizing treatment processes. The CBR system enables the generating of inpatient... Sample PDF
Case Based Reasoning for Customizing Treatment Processes
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Chapter 25
I. Apostolakis, A. Chryssanthou, I. Varlamis
A significant issue in health related applications is protecting a patient’s profile data from unauthorized access. In the case of telemedicine... Sample PDF
A Holistic Perspective of Security in Health Related Virtual Communities
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Chapter 26
Stamatia Ilioudi
This chapter aims to present various virtual learning environments for medical purposes in the world. More than ever, medical students and... Sample PDF
Virtual Learning Environments in Health
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Chapter 27
Jelena Vucetic
In the last decade, advances in medicine, telemedicine, computer technologies, information systems, Web applications, robotics and... Sample PDF
Multimedia Distance Learning Solutions for Surgery
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Chapter 28
Maria Andréia F. Rodrigues
This chapter shows how recent computing technologies such as collaborative virtual environments, high speed networks and mobile devices can be used... Sample PDF
Collaborative Virtual Environments and Multimedia Communication Technologies in Healthcare
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Chapter 29
Tiffany A. Koszalka, Bradley Olson
A major issue facing medical education training programs across the USA is the recent advent of universal mandatory duty hour limitations and the... Sample PDF
Transforming a Pediatrics Lecture Series to Online Instruction
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Chapter 30
Anastasia N. Kastania, Stelios Zimeras
In this chapter the authors investigate telehealth quality and reliability assurance. Various models and standards can be applied to assess software... Sample PDF
Quality and Reliability Aspects in Telehealth Systems
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Chapter 31
Kleopatra Alamantariotou
Recent statistics show that the World Wide Web has now grown to over 100 million sites: a phenomenal expansion in only 15 years (Mulligan 2007). It... Sample PDF
Quality of Health Information on the Internet
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Chapter 32
Kashif Hussain
This chapter provides a practical approach to computerized system validation (CSV) for the pharmaceutical organizations for the users dealing with... Sample PDF
A Practical Approach to Computerized System Validation
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Chapter 33
Bill Ag Drougas, Maria Sevdali
Ergophysiology as a division of the Physiology and helps us today to understand what happens in the human body and movement and how we are able to... Sample PDF
Organization and Evaluation of Experimental Measurements of Ergophysiological Data with the Method of SF12V2
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Chapter 34
Daniele Apiletti
Current advances in sensing devices and wireless technologies are providing a high opportunity for improving care quality and reducing the medical... Sample PDF
Ubiquitous Risk Analysis of Physiological Data
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Chapter 35
Manfred Doepp
In our energy diagnostic department we noticed more and more cases with irrational stimulus-reaction- patterns and with a chaotic regulation state... Sample PDF
Chaotization of Human Systems by Technical Electromagnetic Fields
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Chapter 36
Mary Schmeida, Ramona McNeal
This chapter is an analysis of demographic variables influencing policy outcomes with online health information searches in the general U.S. public.... Sample PDF
Demographic Differences in Telehealth Policy Outcomes
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About the Contributors