INFORMATION RETRIEVAL A Biomedical and Health Perspective 4th Edition William Hersh Full Chapters Instanly
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William Hersh
Information
Retrieval:
A Biomedical
and Health
Perspective
Fourth Edition
Health Informatics
This series is directed to healthcare professionals leading the transformation of
healthcare by using information and knowledge. For over 20 years, Health
Informatics has offered a broad range of titles: some address specific professions
such as nursing, medicine, and health administration; others cover special areas of
practice such as trauma and radiology; still other books in the series focus on
interdisciplinary issues, such as the computer based patient record, electronic health
records, and networked healthcare systems. Editors and authors, eminent experts in
their fields, offer their accounts of innovations in health informatics. Increasingly,
these accounts go beyond hardware and software to address the role of information
in influencing the transformation of healthcare delivery systems around the world.
The series also increasingly focuses on the users of the information and systems: the
organizational, behavioral, and societal changes that accompany the diffusion of
information technology in health services environments.
Developments in healthcare delivery are constant; in recent years, bioinformatics
has emerged as a new field in health informatics to support emerging and ongoing
developments in molecular biology. At the same time, further evolution of the field
of health informatics is reflected in the introduction of concepts at the macro or
health systems delivery level with major national initiatives related to electronic
health records (EHR), data standards, and public health informatics.
These changes will continue to shape health services in the twenty-first century.
By making full and creative use of the technology to tame data and to transform
information, Health Informatics will foster the development and use of new
knowledge in healthcare.
Information Retrieval:
A Biomedical and Health
Perspective
Fourth Edition
William Hersh
Oregon Health & Science University
Portland, OR
USA
This Springer imprint is published by the registered company Springer Nature Switzerland AG
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
To Sally, Becca, Alyssa, and AJ
Preface
The main goal of this book is to provide an understanding of the theory, implemen-
tation, and evaluation of information retrieval (IR) systems in biomedicine and
health. There is already a great deal of “how-to” information on searching for bio-
medical and health information (some listed in Chap. 1). Similarly, there are also a
number of high-quality basic IR textbooks (also listed in Chap. 1). This volume is
different from all of the above in that it covers basic IR as do the latter books, but
with a distinct focus on the biomedical and health domain.
The first three editions of this book were published in 1996, 2003, and 2009.
Although subsequent editions of books in many fields represent incremental
updates, this edition is profoundly rewritten and is essentially a new book. The IR
world has changed substantially since I wrote the first three editions of the book. At
the time of the first edition, IR systems were available and not too difficult to access
if you had the means and expertise. Also, in that edition, the Internet was a “special
topic” in the very last chapter of the book. By the second edition, the World Wide
Web had become a widespread platform for the use of information access and deliv-
ery, but had not achieved the nearly ubiquitous and saturated use it has now. At
present, however, not only must health care professionals and biomedical research-
ers understand how to use IR systems to be effective in their work, but patients and
consumers must also as well to attain optimal health care.
Similar to previous editions will be the maintenance of a Web site for errata and
updates. The Website http://www.irbook.info/ will identify all errors in the book
text as well as provide updates on important new findings in the field as they become
available.
As in the first three editions, the approach is still to introduce all the necessary
theory to allow coverage of the implementation and evaluation of IR systems in
biomedicine and health. Any book on theoretical aspects must necessarily use tech-
nical jargon, and this book is no exception. Although jargon is minimized, it cannot
be eliminated without retreating to a more superficial level of coverage. The read-
er’s understanding of the jargon will vary based on their background, but anyone
with some background in computers, libraries, health, and/or biomedicine should be
vii
viii Preface
able to understand most of the terms used. In any case, an attempt to define all jar-
gon terms is made.
Another approach is to attempt wherever possible to classify topics, whether
discussing types of information or models of evaluation. I have always found clas-
sification useful in providing an overview of complex topics. One problem, of
course, is that everything does not fit into the neat and simple categories of the clas-
sification. This occurs repeatedly with IR, and the reader is forewarned.
This book had its origins in a tutorial taught at the former Symposium on
Computer Applications in Medicine (SCAMC) meeting. The content continues to
grow each year through my course taught to biomedical informatics students in the
on-campus and disease-learning programs at OHSU. (Students often do not realize
that next year’s course content is based in part on the new and interesting things they
teach me!) The book can be used in either a basic information science course or a
biomedical and health informatics course. It should also provide a strong back-
ground for others interested in this topic, including those who design, implement,
use, and evaluate IR systems.
Interest continues to grow in biomedical and health IR systems. I entered a fel-
lowship in medical informatics at Harvard University in the late 1980s, during the
initial era of medical artificial intelligence. I had assumed I would take up the ban-
ner of some aspect of that area, such as knowledge representation. But along the
way I came across a reference from the field of “information retrieval.” It looked
interesting, so I looked at the references of that reference. It did not take long to
figure out that this was where my real interests lay, and I spent many an afternoon
in my fellowship tracing references in the Harvard University and Massachusetts
Institute of Technology libraries. Even though I had not yet heard of the field of
bibliometrics, I was personally validating all its principles. Like many in the field, I
have been amazed to see IR become so “mainstream” with its routine use by almost
everyone on the planet.
The book is divided into eight chapters. Chapter 1 provides basic definitions and
models that will be used throughout the book. It also points to resources for the field
and introduces evaluation of systems. Chapter 2 provides an overview of biomedical
and health information, describing some of the issues in its production, dissemina-
tion, and use. Chapter 3 gives an overview of the great deal of content that is cur-
rently available. Chapters 4 and 5 cover the two fundamental intellectual tasks of
IR, indexing and retrieval, with the predominant paradigms of each discussed in
detail. Chapter 6 discusses the methods and challenges of larger information access.
Chapter 7 focuses on evaluation research that has been done on state-of-the-art sys-
tems in the biomedical and health domain. Finally, Chapter 8 explores research
about IR systems and their users, with an emphasis on applications in the biomedi-
cal and health domain. Within each chapter, the goal is to provide a comprehensive
overview of the topic, with thorough citations of pertinent references. There is a
preference for discussing biomedical and health implementations of principles, but
where this is not possible, the original domain of implementation is discussed.
This book would not have been possible without the influence of various men-
tors, dating back to high school, who nurtured my interests in science generally
Preface ix
1 Foundations���������������������������������������������������������������������������������������������� 1
1.1 Basic Definitions������������������������������������������������������������������������������ 3
1.2 Scientific Disciplines Concerned with IR ���������������������������������������� 5
1.3 Models of IR ������������������������������������������������������������������������������������ 7
1.3.1 The Information World �������������������������������������������������������� 7
1.3.2 Users ������������������������������������������������������������������������������������ 8
1.3.3 Health Decision-Making������������������������������������������������������ 9
1.3.4 Knowledge Acquisition and Use������������������������������������������ 9
1.4 IR Resources ������������������������������������������������������������������������������������ 11
1.4.1 Organizations������������������������������������������������������������������������ 11
1.4.2 Journals �������������������������������������������������������������������������������� 12
1.4.3 Texts�������������������������������������������������������������������������������������� 13
1.4.4 Tools�������������������������������������������������������������������������������������� 13
1.5 The Internet and World Wide Web���������������������������������������������������� 14
1.5.1 Users ������������������������������������������������������������������������������������ 15
1.5.2 Usage������������������������������������������������������������������������������������ 16
1.5.3 Hypertext and Linking���������������������������������������������������������� 18
1.6 Evaluation ���������������������������������������������������������������������������������������� 19
1.6.1 Classification of Evaluation�������������������������������������������������� 21
1.6.2 Relevance-Based Evaluation������������������������������������������������ 24
1.6.3 Challenge Evaluations���������������������������������������������������������� 30
References�������������������������������������������������������������������������������������������������� 34
2 Information���������������������������������������������������������������������������������������������� 41
2.1 What Is Information?������������������������������������������������������������������������ 41
2.2 Theories of Information�������������������������������������������������������������������� 42
2.3 Properties of Scientific Information�������������������������������������������������� 45
2.3.1 Growth���������������������������������������������������������������������������������� 45
2.3.2 Obsolescence������������������������������������������������������������������������ 46
2.3.3 Fragmentation ���������������������������������������������������������������������� 48
xi
xii Contents
4 Indexing���������������������������������������������������������������������������������������������������� 181
4.1 Types of Indexing������������������������������������������������������������������������������ 181
4.2 Factors Influencing Indexing������������������������������������������������������������ 182
4.3 Controlled Vocabularies�������������������������������������������������������������������� 183
4.3.1 General Principles of Controlled Vocabularies �������������������� 184
4.3.2 The Medical Subject Headings (MeSH) Vocabulary������������ 185
4.3.3 Other Indexing Vocabularies������������������������������������������������ 191
4.3.4 The Unified Medical Language System�������������������������������� 194
4.4 Manual Indexing ������������������������������������������������������������������������������ 197
4.4.1 Bibliographic Manual Indexing�������������������������������������������� 198
4.4.2 Full-Text Manual Indexing �������������������������������������������������� 200
4.4.3 Web Manual Indexing���������������������������������������������������������� 200
4.4.4 Limitations of Manual Indexing ������������������������������������������ 206
4.5 Automated Indexing�������������������������������������������������������������������������� 207
4.5.1 Word Indexing���������������������������������������������������������������������� 207
4.5.2 Limitations of Word Indexing���������������������������������������������� 207
4.5.3 Word Weighting�������������������������������������������������������������������� 208
4.5.4 Link-Based Indexing������������������������������������������������������������ 212
4.5.5 Web Crawling ���������������������������������������������������������������������� 213
4.6 Indexing Annotated Content ������������������������������������������������������������ 214
4.6.1 Index Imaging ���������������������������������������������������������������������� 214
4.6.2 Indexing Learning Objects���������������������������������������������������� 215
4.6.3 Indexing Biomedical and Health Data���������������������������������� 218
4.7 Data Structures for Efficient Retrieval���������������������������������������������� 218
References�������������������������������������������������������������������������������������������������� 220
5 Retrieval���������������������������������������������������������������������������������������������������� 225
5.1 Search Process���������������������������������������������������������������������������������� 226
5.2 General Principles of Searching�������������������������������������������������������� 226
5.2.1 Exact-Match Searching�������������������������������������������������������� 227
5.2.2 Partial-Match Searching�������������������������������������������������������� 229
5.2.3 Term Selection���������������������������������������������������������������������� 233
5.2.4 Other Attribute Selection������������������������������������������������������ 237
5.3 Searching Interfaces�������������������������������������������������������������������������� 237
5.3.1 Bibliographic������������������������������������������������������������������������ 237
5.3.2 Full Text�������������������������������������������������������������������������������� 249
5.3.3 Annotated������������������������������������������������������������������������������ 252
5.3.4 Aggregations ������������������������������������������������������������������������ 257
5.4 Document Delivery �������������������������������������������������������������������������� 257
5.5 Notification or Information Filtering������������������������������������������������ 258
References�������������������������������������������������������������������������������������������������� 259
6 Access�������������������������������������������������������������������������������������������������������� 261
6.1 Libraries�������������������������������������������������������������������������������������������� 261
6.1.1 Definitions and Functions of DLs ���������������������������������������� 263
6.2 Access to Content ���������������������������������������������������������������������������� 265
xiv Contents
Index������������������������������������������������������������������������������������������������������������������ 407
Chapter 1
Foundations
The goal of this book is to present the field of information retrieval (IR), sometimes
called search, with an emphasis on the biomedical and health domain. To many,
“information retrieval” implies retrieving information of any type from a computer.
However, to those working in the field, IR has a different, more specific meaning,
which is the retrieval of information from databases that predominantly contain
textual information. A field at the intersection of information science and computer
science, IR concerns itself with the indexing and retrieval of information from het-
erogeneous and mostly textual information resources. The term was coined by
Mooers in 1951, who advocated that it be applied to the “intellectual aspects” of
description of information and systems for its searching [1].
The advancement of computer technology continues to alter the nature of IR. As
recently as the 1970s, Lancaster stated that an IR system does not inform the user
about a subject; it merely indicates the existence (or nonexistence) and whereabouts
of documents related to an information request [2]. At that time, of course, comput-
ers had considerably less power and storage than today’s personal computers, and
there was no Internet connecting the world’s computers and other information
devices to each other. In the 1970s, computers and network systems were only suf-
ficient to handle bibliographic databases, which contained just the title, source, and
a few indexing terms for documents. Furthermore, the high cost of computer hard-
ware and telecommunications usually made it prohibitively expensive for end users
to directly access such systems, so they had to submit requests that were run in
batches and returned hours to days later.
In the twenty-first century, however, the state of computers and IR systems is
much different, leading to new perspectives on the nature of the field [3, 4]. End-
user access to massive amounts of information in databases and on the World Wide
Web is routine. A recent monograph traces the history of IR from early experiments
in the 1960s through the advent of ubiquitous search systems in the 2000s [5].
Not only can IR databases contain the full text of resources, but they may also
contain images, sounds, and even video sequences. Indeed, there is now the notion
of the digital library, where journals and books are mostly provided in digital form
and library buildings are augmented by far-reaching computer networks [6, 7]. The
scientific publishing enterprise has been transformed to increasingly open science,
with access not only to research publications but also their underlying data [8]. New
models for delivering knowledge have been proposed, such as the Mobilizing
Computable Biomedical Knowledge initiative, whose manifesto calls for knowl-
edge to be provided in “computable formats that can be shared and integrated into
health information systems and applications” [9].
So transformative and ubiquitous has IR become that the name of the leading
Web search engine, Google, has entered the vernacular in a variety of ways, includ-
ing as a verb (i.e., using a search engine to look something up is called “Googling”)
[10]. The Google Trends1 (formerly Zeitgeist) keeps a tally of the world’s interests
as measured by what humans collectively type into the Google search engine. In
addition, some lament that the “Google generation,” i.e., today’s legions of technol-
ogy-savvy young people, are not critical enough in their skills regarding seeking,
synthesizing, and critically analyzing information [11].
One of the early motivations for IR systems was the ability to improve access to
information. Noting that the work of early geneticist Gregor Mendel was undiscov-
ered for nearly 30 years, Vannevar Bush called in the 1960s for science to create
better means of accessing scientific information [12]. In current times, there is equal
if not more concern with “information overload” and how to avoid missing impor-
tant information. A well-known example occurred when a patient who died in a
clinical trial in 2000 might have survived if information about the toxicity of the
agent being studied from the 1950s (before the advent of MEDLINE) had been
more readily accessible [13]. Indeed, a major challenge in IR is helping users find
“what they don’t know” [14].
Just how much information is out there? One analysis estimated the amount of
digital data in the world to be 33 zettabytes in 2018, with a projection to grow to 175
zettabytes by 2025 [15]. (A zettabyte is 1021 bytes, or one billion terabytes.) Another
report estimated the amount of computer network traffic to triple between 2017 and
2022 to 4.8 zettabytes per year, which would be about equal to all previous Internet
traffic from 1984 to 2018 [16]. Another analysis noted that 3.8 million searches of
Google are done every minute [17]. In the 2000s, Card published a figure comparing
the exponential growth of information as it surpassed the estimate of the size of all
documents created in human history (40,000 years), well above the estimated
amount of information a human could learn in a year (see Fig. 1.1) [18]. A current
estimate of the health information on a single human over their lifetime is over 1000
terabytes, with the major of information coming from social determinants of health
and health behaviors, and only a tiny fraction representing clinical data (<1 tera-
byte) [19]. Of course, only a small part of this data is the kind of text and other
information we might wish to retrieve using an IR system. Nonetheless, it was
estimated in 2016 that Google had indexed 130 trillion Web pages in its search
engine [20].
1
https://trends.google.com
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