Journal of the AmericanShortliffe

Medical Informatics
EH. J Am Association
Med Inform Assoc 2016;0:1–4. Advance Access
doi:10.1093/jamia/ocw074, Perspective published June 6, 2016

RECEIVED 28 October 2015

The organization and content of informatics REVISED 15 April 2016
ACCEPTED 19 April 2016
doctoral dissertations
Edward H Shortliffe
ABSTRACT
....................................................................................................................................................
This article offers suggested guidelines for graduate students who are embarking on informatics doctoral studies and anticipating the dissertation
research and its documentation. Much of the guidance is pertinent for writing dissertations in other disciplines as well. The messages are largely
directed at doctoral students, but some elements are also pertinent for master’s students. All are relevant for faculty research advisors. The value
of the dissertation is often underestimated. Too often it is seen as a hurdle to be overcome rather than an opportunity to gain insight into one’s
own research and to learn how to communicate effectively about it. Ideas that have been ill-formed often do not gel effectively until one tries to
write about them. The main lesson is that the preparation of a carefully crafted, rigorous, logically evidence-based, and influential dissertation can
be remarkably rewarding, both personally and professionally.
....................................................................................................................................................
Keywords: academic dissertations, informatics education, research report, writing, authorship

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INTRODUCTION
Few aspects of graduate education are as challenging and anxiety-
producing as the successful writing and defense of the doctoral
dissertation. Yet students often claim that they are given very little
guidance about the process, especially with regard to the actual writ-
ing, format, and content of the formal document. There are books on
the topic1–5 and services that will help students write their disserta-
tion.6 An Internet search provides several university websites with
dissertation-preparation advice, yet the biomedical literature appears
to be devoid of articles on the subject. The sources cited above are ge-
neric and provide only high-level guidance when a trainee is writing a
dissertation. Advice that may apply equally to dissertations in the hu-
manities, social sciences, engineering, and life sciences may have
limited value for a student who needs to adapt the organization and
writing to the characteristics of a specific scientific discipline.
with one informatics dissertation completed by a PhD student in 1990.
That document went on to be published as a book7 and to win the an-
nual doctoral dissertation award from the Association for Computing
Machinery.8 The perspectives I offer are personal preferences and ad-
vice, but are based on decades of guiding roughly 200 graduate stu-
dents through their research projects and, for many, the writing of a
dissertation. These are not drawn from generic references but are,
rather, based on personal experience as I have sought to develop
guidelines for my students. The messages here are largely directed at
doctoral students, but some elements are pertinent for master’s stu-
dents as well. All are relevant for faculty research advisors. The main
lesson is that the preparation of a carefully crafted, rigorous, logically
evidence-based, and influential dissertation can be remarkably re-
warding, both personally and professionally.
The last years of graduate work provide a unique opportunity:
coursework is over, the research is maturing, and the student should

The challenges may be exacerbated in biomedical informatics,
where the field is young and the examples for students to emulate
may be limited at their own institution. Furthermore, informatics is, by
its nature, motivated by applications and by the needs of the world of
biomedicine. Many informatics dissertations address a substantive
problem in biomedicine, yet the dissertation cannot simply present a
solution to that applied problem but must also identify how the work
contributes to the underlying science of the informatics discipline.
In this article, I offer some suggested guidelines for graduate stu-
dents who are embarking on informatics doctoral studies and antici-
pating their dissertation research and its documentation. What follows
is intended to be pertinent for informatics dissertations that address
either social science or engineering science topics and innovations.
The emphasis is on pragmatic advice rather than generalizations, al-
though much of what follows might also be pertinent for dissertations
in other fields, and especially those that represent the component sci-
ences included in the informatics domain (eg, computer science, deci-
sion science, cognitive science, information science, and the like). In
fact, excellent dissertations in biomedical informatics may well attract
the attention of scientists in the component discipline, as occurred
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have a singleness of purpose and be fully consumed by the research
and the dissertation. In fact, as most postgraduates can attest, those
few years may be the last time that trainees will have the luxury of fo-
cusing their work and their thinking almost completely on a single ac-
tivity. It is accordingly the responsibility of faculty members to make
sure that students are protected from other demands and distractions
so that the full potential of their work, and the attendant lessons, can
be achieved.
SCIENTIFIC WRITING SKILLS
The value of the dissertation is often underestimated. Too often it is
seen as a hurdle to be overcome rather than an opportunity to gain in-
sight into one’s own research and to learn how to communicate effec-
tively about it. Ideas that have been ill-formed often do not gel
effectively until one tries to write about them. The writing process
forces a more organized and logical perspective, encouraging trainees
to be sure that they have mastered the related literature and can avoid
creating new terms for ideas or concepts that have already been given
established names by others.

Correspondence to Edward H Shortliffe, MD, PhD, MACP, FACMI, College of Health Solutions, Arizona State University, Health North Building, Fifth Floor, 550 N Third
St, Phoenix, AZ 85004 USA. Email: ted.shortliffe@asu.edu. Preferred (permanent) mailing address: 272 W 107th St, APT 5B, New York, NY 10025-7833, USA;
ted@shortliffe.net; Tel: 917-640-0933.
C The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.
V
For Permissions, please email: journals.permissions@oup.com

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 Shortliffe EH. J Am Med Inform Assoc 2016;0:1–4. doi:10.1093/jamia/ocw074, Perspective
Students must learn how to write scientific papers and documents
that are clear, logically organized, interesting to a variety of readers,
well-motivated, evidence-based, and associated with an identified
message or take-home lessons for readers. These skills should be
learned and solidified in graduate school. I generally advise students
to get writing help (and have raised funds to allow one of my programs
to offer professional editing assistance, with an emphasis on develop-
mental editing rather than copy editing; ie, on the overall logical flow
and content of one’s writing, not just the grammatical details). This
advice holds for both international students and those for whom
English is their first language. Regardless of whether the trainee is
aiming for academia, industry, a research lab, or another professional
setting, writing skills are crucial throughout one’s career.
Getting Practice before the Dissertation
Although all graduate students will have written course papers as un-
dergraduates, the skill sets for scientific writing are somewhat differ-
ent. As a result, it is important to start writing early in graduate
school, even before a dissertation topic has been defined. Write up
early project work for conferences or, when suitable, for journals.
Work closely with experienced faculty who can critique the writing. If a
dissertation topic emerges from such early work, some portions of
early papers may be reusable for elements of the dissertation.
However, despite the trend in some fields that have downplayed the
importance of the dissertation if one has published papers, I personally
avoid the notion that a dissertation can be a selection of previously
published papers “stapled” together. The dissertation is the trainee’s
magnum opus, on which writing skills can be solidified and reputa-
tions made. It provides trainees with a chance to offer a coherent, syn-
thetic perspective on the entire body of their doctoral work. If a
department or institution accepts a set of published papers as the doc-
umentation of doctoral work, I would encourage the student to blend
them as chapters into a final summary document that synthesizes the
topic across the published papers and summarizes the total body of
work, its importance, its future, and its contribution to informatics.
By the time one is writing a dissertation, there should be no excuse
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for grammatical or spelling errors or problems with word use.
Typographical errors in the final version indicate inadequate proof-
reading, make the author look sloppy, and detract from the reader’s
impressions of the work. The dissertation may be the last formal op-
portunity for trainees to instill rigorous habits and lessons, which will
serve them well throughout their careers.
WRITING THE DISSERTATION
The goal is to write a dissertation that others will want to read. It is im-
portant to acknowledge, however, that not all readers will understand
certain technical components. Accordingly, one should provide a road
map so that less technical readers can skip some of the details but
still appreciate the work. I encourage students to use the first chapter
to fascinate readers with the work, thereby encouraging them to keep
reading so that they will learn how it was done!
Bear in mind that a doctoral student in biomedical informatics is
supposed to make a clear contribution to informatics, not just to the
domain of the research application. Thus, descriptions of computing
systems or other artifacts may be of interest, and may even be cru-
cially important to include in the document, but the application itself is
not the contribution of the work to the science of the field. What is the
underlying method, idea, or theory that the application represents?
How does it generalize to other applications? A great clinical applica-
tion may be suitable for publication in a clinical journal, but the
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dissertation topic should be the novel contribution that allows that ap-
plication to be built.
Organization of the Dissertation Document
Given the background laid out above, how should a dissertation be or-
ganized? I have developed several suggestions over the years and
share them here for others to follow or adapt as appropriate. Bear in
mind that the precise topic of the dissertation will require adjustments
to what is proposed generically here.
The dissertation needs to tell an engaging story, even though it is
a scientific document. Plan the writing with that story in mind, and
think about how best to convey what has been accomplished and how
it can contribute to future work by others. Table 1 provides a synopsis
of the key elements, some of which are clarified further below.
The title for the dissertation should make it clear that this is an in-
formatics topic and should not simply focus on the motivating applica-
tion. I have seen many informatics theses that convey excitement
about a solution to a motivating application but make almost no men-
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tion of the specific informatics contribution in their title or abstract. For
example, if a student writes a dissertation saying that the main contri-
bution of the research is a biologic or genetic discovery, then perhaps
he or she should have pursued a PhD in biology or genetics. An infor-
matics dissertation needs to emphasize contributions to the informat-
ics discipline, as important as that biological discovery may be. Thus
the abstract, which should be written at the end when all other work
is complete, should convey the informatics innovation as well as any
application that was developed using that informatics work.
Chapter 1 is arguably the most important chapter in the disserta-
tion. It will typically be written at the beginning and then revised itera-
tively as the document develops. I urge students to state their
hypothesis within the first few pages, highlighting it in italics. That
statement will guide the rest of the exposition, orient the reader to
what the student has done, and lead to the assumption that success
Figure 1. An example of an architectural diagram for a ge-
neric decision-support system. Such a diagram might, for
example, be inserted into Chapter 3 of the dissertation (see
text). It shows the system components, including the innova-
tive contribution outlined in Chapter 3, and indicates that the
other key components, and their use of the new methods,
will be discussed in Chapters 4 and 5.
 Shortliffe EH. J Am Med Inform Assoc 2016;0:1–4. doi:10.1093/jamia/ocw074, Perspective
Table 1: Organization and components of a generic biomedi-
cal informatics doctoral dissertation. See text for discussion.
Typically n is between 7 and 9.
Dissertation Key Considerations and Content
Element
Title • Play down motivating application
• Play up innovative informatics contribution
Abstract • Convey nature of innovative contribution
• Mention motivating application
•
Summarize validation or evaluation
• Write this summary last, when document is
mature
Chapter 1 • Introduction
• Statement of hypothesis (highlight in bold or
italics)
• Motivation and aims
• Relevance to biomedicine or health
• Overview of research and document
•
Road map
Chapter 2 • Selective literature review
• Assessment of gaps in prior work
• Delineation of contributions of dissertation re-
search in light of gaps
Chapter 3 • Presentation of the new idea (method or theory)
in detail
• Overview of any application developed
• Explanation of Chapters 4 to n 2
• Inclusion of explanatory diagram (Figure 1)
Chapters 4 • Technical presentation of components or
to n . 2 subtopics
..
Chapter n 1 • Evaluation (or demonstration of the validity and/
or impact) of the new idea from Chapter 3
Chapter n • Summary of accomplishments and contributions
• Assessment of hypothesis (from Chapter 1) in
light of what has been discussed
• Generalizability of the results
•
Range of applicability
•
Future work
• Conclusions
in assessing it will be summarized in the final chapter. Chapter 1
needs to capture readers and bring them into the rest of the docu-
ment. Still, many readers will focus solely on the first and last chapters
in the document, and the author needs to bear this in mind when writ-
ing those chapters in particular.
Chapter 2 is traditionally the literature review. It should be guided
by the hypothesis from Chapter 1 and anticipate the delineation of the
problems with current approaches that the author tackles with new
methods or theories in subsequent chapters. The review should avoid
being overly broad and should focus primarily on those components of
the literature that are most pertinent to the hypothesis, the anticipated
contribution of the work, and the alternate approaches and their limita-
tions that the student is attempting to address.
The number of chapters (call it n) in a dissertation will vary, but is
typically between 7 and 9. Chapter 3 introduces the methodologic
innovation or theory that is the main contribution of the work.
Chapters 4 to n 2 then lay out the subtopics or components that
demonstrate the utility of the innovative contribution. Thus Chapter 3
needs to provide an overview of the chapters that follow. One way to
do this is with a diagram that shows the overall nature of the work
and then indicates, on the diagram, which elements are covered in
which chapter. In Figure 1, as an example, a generic computer system
that deals with uncertainty modeling in knowledge bases is shown di-
agrammatically, with components and logical flow shown. In the cor-
responding dissertation’s Chapter 3, the diagram would show what
has been introduced in the current chapter (labeled “uncertainty man-
agement system” and “knowledge base” in the diagram) and then
show the components that are discussed in Chapters 4 and 5 (see dia-
gram). The number of discrete topics or components will determine
how many chapters follow Chapter 3. The corresponding diagram for
a dissertation that is focused more on social science methods would
be different but ideally would still capture the logical flow of the work
and how the subsequent chapters relate to the total effort.
The next to last chapter (Chapter n 1) is typically the evaluation
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or demonstration of validity. The nature of this chapter can vary widely
depending on the type of work. The focus is not simply on the motivat-
ing application but on the effectiveness of the underlying innovative
methodology or theory that is the topic of the dissertation.
Chapter n, then, is the final discussion that summarizes the re-
sults, the contribution of the work, and the assessment of the initial
hypothesis, and lays out what lies ahead. A specific discussion of the
generalizability of the method and its range of its applicability is to be
encouraged. The author should bear in mind that a reader may have
fully digested only Chapter 1 before reading Chapter n.
CONCLUSIONS
The discussion here has necessarily been very general, and individual
students will need to adapt these guidelines to the specifics of their
own research topic and experimental approach. But the general no-
tions do apply broadly. The effort implied is not wasted. Although only
a few dissertations will be published formally as books,7 the lessons
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learned in writing one will serve the graduate well, regardless of the
career path. And much that is written in the document, if not previ-
ously published, can be extracted and adapted for formal publication
in peer-reviewed journals. For example, Chapter 2 is often a great
source of content that can be edited into an influential review paper
suitable for publishing.
Most important, the more students apply the proposed rigorous
approach to dissertation preparation and writing, the more graduates
will understand and continue to contribute to the scientific base of the
biomedical informatics discipline. Wonderful applications will always
be needed, but they depend on scientific advances that need to be
well identified and articulated, both in talks and in writing. Everyone in
both the basic research environment and applied settings will benefit
when the scientific base for informatics is strengthened.
COMPETING INTERESTS
No competing interests to report.
ACKNOWLEDGEMENTS
The author gratefully acknowledges the contributions of informatics graduate
students over more than 3 decades. The teacher learns from his students, and
much of what is summarized in this article was taught through vibrant interac-
tions with doctoral students as they strove to write effective and influential
dissertations.
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 Shortliffe EH. J Am Med Inform Assoc 2016;0:1–4. doi:10.1093/jamia/ocw074, Perspective

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AUTHOR AFFILIATIONS
....................................................................................................................................................
Biomedical Informatics, College of Health Solutions, Arizona State University,
Phoenix, AZ USA; Biomedical Informatics, College of Physicians and Surgeons,
Columbia University, New York, NY USA; Health Policy and Research (Health
Informatics), Weill Cornell Medical College, New York, NY USA

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