Practical Pathology Informatics: Demystifying informatics for the practicing anatomic pathologist

406 Pages·2005·28.9 MB·English

by  John H. Sinard

PRACTICAL PATHOLOGY INFORMATICS
PRACTICAL PATHOLOGY INFORMATICS
Demystifying informatics for the practicing
anatomic pathologist
John H. Sinard, MD, PhD
Director, Pathology Informatics Program
Department of Pathology
Yale University School of Medicine
New Haven, CT
Springer
John H. Sinard, MD, PhD
Director, Pathology Informatics Program
Department of Pathology
Yale University School of Medicine
New Haven, CT
USA
Library of Congress Cataloging-in-Publication Data
Sinard, John H.
Practical pathology informatics : demystifying informatics for the practicing anatomic
pathologist / John H. Sinard.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-0-387-28057-8 (alk. paper)
ISBN-10: 0-387-28057-X (alk. paper)
1. Pathology. 2. Medical informatics. 3. Anatomy, Pathological. I. Title.
[DNLM: 1. Medical Informatics—methods. 2. Pathology—methods. QZ 26.5 S615p 2005]
RB25.S52 2005
65.5’04261—dc22 2005050011
ISBN -10 0-387-28057-X e-ISBN 0-387-28058-8
ISBN -13 978-0-387-28057-8 e-ISBN 978-0-387-28058-5
Printed on acid-free paper.
© 2006 Springer Science+Business Media, Inc.
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Printed in the United States of America.
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This book is dedicated to my nieces and nephews:
Thomas, Rebecca, Claire, and Andrew
Contributing Author
(Chapter 11):
Michael Krauthammer, MD, PhD
Department of Pathology
Yale University School of Medicine
New Haven, CT
Preface
Almost all areas of intellectual pursuit in which there is an element of
subjectivity share an interesting internal paradox. At first exposure, the field
is a complete mystery. Then, as one acquires some of the domain
knowledge and learns about the rules, the field starts to make sense, and
before long may even seem trivial. However, as one delves deeper and
acquires experience, complexities and subtleties begin to re-emerge, as well
as realization of the validity of some of the exceptions to the rules, and the
field is suddenly less obvious and clear than it was before. This is the value
of experience; this is where true insight starts to emerge. Informatics shares
this internal paradox. When I peruse the books available on informatics, it is
this insight which I am seeking. The details of the data I can look up on the
internet, but the insight is harder to find, and only comes from having
developed and implemented (or at least tried to implement) various
solutions. It would be absurd to suggest that any one solution, no matter how
successful in a particular environment, will work well in every other
environment, and I personally question the insight of any author who claims
that a particular solution to an information management problem is the one
right solution. Of course, insight can only be presented in the context of
information. This book is a mixture of information, interpretation,
perspective, and, I would like to think, a little insight.
When I lecture or give a conference to pathology residents about gross,
autopsy, or ophthalmic pathology, I have a pretty good idea going in what
level of knowledge I can expect from my audience, from the first year
residents up through the fellows. Lecturing on informatics topics, however,
is more difficult, not because the material is any more esoteric, but rather
because the range of knowledge of my audience can be enormous: some
have already designed and deployed complete computer-based solutions to
some problem, while others still approach the keyboard and mouse with
some degree of apprehension. The target audience for this book is equally
broad. Designed around the curriculum I developed for teaching informatics
Practical Patholo^ Informatics
to pathology residents, the goal of this book is to introduce and demystify a
variety of topics in the broad discipline of pathology informatics. In no way
have I attempted to cover the entire scope of this discipline, but rather have
focused on issues of particular relevance to the practicing anatomic
pathologist. It is not my intention to turn anyone into an informatician
(?informaticist?). Rather, I hope to provide the reader with enough
information about the pros and cons of various elements of the field, and to
share some insight into their complexity, so that the reader will be able to
evaluate the topic in an educated fashion. It is up to the reader to weigh the
competing factors presented and then, tempered with an understanding of
their own unique environment, to make an individualized assessment as to
the best approach from the perspective of their needs.
Toward that end, what follows are multiple relatively short chapters, each
introducing and discussing some aspect of pathology informatics. The
scope, in my opinion, represents the fund of knowledge with which a typical
practicing pathologist should be familiar. In fact, the early chapters contain
basic information about computers and databases which is applicable to any
discipline, with the later chapters containing more anatomic pathology
specific topics. The scope of this text would also be an appropriate core for
residency training in pathology informatics. In an attempt to appeal to a
broader audience, I have included both basic as well as some less basic
information. Since I have always felt that it is better to understand
something than to simply memorize it, the detail provided is sufficient for
the reader to obtain an understanding of the topic being presented. I have
also included, where appropriate, my views of the pros and cons behind the
more controversial aspects of each topic. For the most part, I present
information and analysis (although I must confess that the first and last
chapters are really more like editorials). The chapters can be read in any
order. Each chapter is divided into several short sections. If at any point a
section drifts into the "too obscure", simply go on to the next section.
Throughout the discussions, I will not recommend specific vendors or
products, but rather focus on general principles and processes which will
remain applicable as the vendors and products come and go. If each reader
takes away at least a different perspective on the breath of pathology
informatics, its role as a tool in the daily practice of pathology, and an
appreciation for how informatics will be key in shaping the way we practice
medicine in the future, I will consider my efforts in writing this book worth
while.
Acknowledgments
First, I would like to thank my informal consultants, the members of the
operational informatics unit of Yale Pathology, for helping to create an
environment which allowed me to pursue my interests in this area, as well as
for working hard enough to give me the time to write this book. These
include Agatha Daley, Peter Gershkovich, Katie Henderson, Janos Lobb,
Brian Paquin, Sophia Gyory, Emma Walz-Vaitkus, and Mark Mattie.
Secondly, 1 want to thank the residents of the Anatomic Pathology
Residency Training Program at Yale-New Haven Hospital for giving me a
forum to "try out" some of my material, and for consistently reminding me
of the importance of informatics training for our future pathologists. In
particular, thanks to Yuri Fedoriw, my first "informatics rotation" resident,
for input and suggestions which helped me get through some of the more
difficult parts of this book. Similarly, thanks to Wally Henricks for helpful
comments on a portion of this book, and Jon Morrow for many discussions
on the future of pathology informatics. Finally, I want to thank the
anonymous person who, on their evaluation of the first presentation of my
informatics short course at the United States and Canadian Academy of
Pathology annual meeting, wrote simply "when are you going to write your
book?"
Copyrights and Trademarks
This book contains some specific examples, and as such must refer to
products either copyrighted or trademarked (registered or otherwise) by
various manufacturers. Reference to these products is for educational
purposes only, and is in no way intended to represent advertisement,
endorsement, or any claim of intellectual property on my part. The owners
of these trademarks are acknowledged here rather than throughout the text.
Adobe Systems, Inc.: Postscript, Acrobat, PDF, TIFF, Photoshop
American Medical Association: CPT
Apache Software Foundation, Inc.: Apache
Apple Computer, Inc.: Apple, Macintosh, Mac, OS 9, OS X, PICT, FireWire,
TrueType, Safari, Keynote
Bluetooth SIG, Inc: Bluetooth, Bluetooth logo
Centronics Data Computer Corporation: Centronics
College of American Pathologists: SNOMED, SNOMED II, SNOMED III, SNOMED
RT, SNOMED CT, Checklists
CompuServe, Inc.: GIF
dBase, Inc.: dBase
Dell Computer Corporation: Dell
Eastman Kodak Company: PhotoCD
Health Level Seven, Inc.: HL7
Hewlett-Packard, Inc: HP, DEC, Compaq
Intel, Inc.: Intel, Pentium, Celeron
International Business Machines, Inc.: IBM, DB2, PowerPC, G5, VGA
Iomega, Inc.: Zip
Stephen King and Doubleday, Inc.: Jack Torrance, Overlook Hotel
Lemke Software GmbH: GraphlcConverter
Microsoft Corporation: Microsoft, Windows, NT, Windows XP, Windows 2000,
Windows 98, PowerPoint, Word, MS-DOS, Visual Basic, SQL Server, Outlook,
Internet Explorer, Active Server Pages, ODBC
Motorola, Inc.: Motorola
Mozilla Foundation: Firefox
MySQL AB: mySQL
National Library of Medicine: UMLS, PubMed, MEDLINE