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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
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 with one informatics dissertation completed by a PhD student in 1990.
Few aspects of graduate education are as challenging and anxiety- That document went on to be published as a book7 and to win the an-
producing as the successful writing and defense of the doctoral nual doctoral dissertation award from the Association for Computing
dissertation. Yet students often claim that they are given very little Machinery.8 The perspectives I offer are personal preferences and ad-
guidance about the process, especially with regard to the actual writ- vice, but are based on decades of guiding roughly 200 graduate stu-
ing, format, and content of the formal document. There are books on dents through their research projects and, for many, the writing of a
the topic1–5 and services that will help students write their disserta- dissertation. These are not drawn from generic references but are,
tion.6 An Internet search provides several university websites with rather, based on personal experience as I have sought to develop
dissertation-preparation advice, yet the biomedical literature appears guidelines for my students. The messages here are largely directed at
to be devoid of articles on the subject. The sources cited above are ge- doctoral students, but some elements are pertinent for master’s stu-
neric and provide only high-level guidance when a trainee is writing a dents as well. All are relevant for faculty research advisors. The main
dissertation. Advice that may apply equally to dissertations in the hu- lesson is that the preparation of a carefully crafted, rigorous, logically
manities, social sciences, engineering, and life sciences may have evidence-based, and influential dissertation can be remarkably re-
limited value for a student who needs to adapt the organization and warding, both personally and professionally.
writing to the characteristics of a specific scientific discipline. 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 have a singleness of purpose and be fully consumed by the research
may be limited at their own institution. Furthermore, informatics is, by and the dissertation. In fact, as most postgraduates can attest, those
its nature, motivated by applications and by the needs of the world of few years may be the last time that trainees will have the luxury of fo-
biomedicine. Many informatics dissertations address a substantive cusing their work and their thinking almost completely on a single ac-
problem in biomedicine, yet the dissertation cannot simply present a tivity. It is accordingly the responsibility of faculty members to make
solution to that applied problem but must also identify how the work sure that students are protected from other demands and distractions
contributes to the underlying science of the informatics discipline. so that the full potential of their work, and the attendant lessons, can
In this article, I offer some suggested guidelines for graduate stu- be achieved.
dents who are embarking on informatics doctoral studies and antici-
pating their dissertation research and its documentation. What follows SCIENTIFIC WRITING SKILLS
is intended to be pertinent for informatics dissertations that address The value of the dissertation is often underestimated. Too often it is
either social science or engineering science topics and innovations. seen as a hurdle to be overcome rather than an opportunity to gain in-
The emphasis is on pragmatic advice rather than generalizations, al- sight into one’s own research and to learn how to communicate effec-
though much of what follows might also be pertinent for dissertations tively about it. Ideas that have been ill-formed often do not gel
in other fields, and especially those that represent the component sci- effectively until one tries to write about them. The writing process
ences included in the informatics domain (eg, computer science, deci- forces a more organized and logical perspective, encouraging trainees
sion science, cognitive science, information science, and the like). In to be sure that they have mastered the related literature and can avoid
fact, excellent dissertations in biomedical informatics may well attract creating new terms for ideas or concepts that have already been given
the attention of scientists in the component discipline, as occurred 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: Preferred (permanent) mailing address: 272 W 107th St, APT 5B, New York, NY 10025-7833, USA;; Tel: 917-640-0933.
C The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.
For Permissions, please email:

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 dissertation topic should be the novel contribution that allows that ap-
that are clear, logically organized, interesting to a variety of readers, plication to be built.
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 Organization of the Dissertation Document
to get writing help (and have raised funds to allow one of my programs Given the background laid out above, how should a dissertation be or-
to offer professional editing assistance, with an emphasis on develop- ganized? I have developed several suggestions over the years and
mental editing rather than copy editing; ie, on the overall logical flow share them here for others to follow or adapt as appropriate. Bear in
and content of one’s writing, not just the grammatical details). This mind that the precise topic of the dissertation will require adjustments
advice holds for both international students and those for whom to what is proposed generically here.
English is their first language. Regardless of whether the trainee is The dissertation needs to tell an engaging story, even though it is
aiming for academia, industry, a research lab, or another professional a scientific document. Plan the writing with that story in mind, and
setting, writing skills are crucial throughout one’s career. 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.
Getting Practice before the Dissertation The title for the dissertation should make it clear that this is an in-
Although all graduate students will have written course papers as un- formatics topic and should not simply focus on the motivating applica-
dergraduates, the skill sets for scientific writing are somewhat differ- tion. I have seen many informatics theses that convey excitement
ent. As a result, it is important to start writing early in graduate about a solution to a motivating application but make almost no men-

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school, even before a dissertation topic has been defined. Write up tion of the specific informatics contribution in their title or abstract. For
early project work for conferences or, when suitable, for journals. example, if a student writes a dissertation saying that the main contri-
Work closely with experienced faculty who can critique the writing. If a bution of the research is a biologic or genetic discovery, then perhaps
dissertation topic emerges from such early work, some portions of he or she should have pursued a PhD in biology or genetics. An infor-
early papers may be reusable for elements of the dissertation. matics dissertation needs to emphasize contributions to the informat-
However, despite the trend in some fields that have downplayed the ics discipline, as important as that biological discovery may be. Thus
importance of the dissertation if one has published papers, I personally the abstract, which should be written at the end when all other work
avoid the notion that a dissertation can be a selection of previously is complete, should convey the informatics innovation as well as any
published papers “stapled” together. The dissertation is the trainee’s application that was developed using that informatics work.
magnum opus, on which writing skills can be solidified and reputa- Chapter 1 is arguably the most important chapter in the disserta-
tions made. It provides trainees with a chance to offer a coherent, syn- tion. It will typically be written at the beginning and then revised itera-
thetic perspective on the entire body of their doctoral work. If a tively as the document develops. I urge students to state their
department or institution accepts a set of published papers as the doc- hypothesis within the first few pages, highlighting it in italics. That
umentation of doctoral work, I would encourage the student to blend statement will guide the rest of the exposition, orient the reader to
them as chapters into a final summary document that synthesizes the what the student has done, and lead to the assumption that success
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

Figure 1. An example of an architectural diagram for a ge-

for grammatical or spelling errors or problems with word use. neric decision-support system. Such a diagram might, for
Typographical errors in the final version indicate inadequate proof- example, be inserted into Chapter 3 of the dissertation (see
reading, make the author look sloppy, and detract from the reader’s text). It shows the system components, including the innova-
impressions of the work. The dissertation may be the last formal op- tive contribution outlined in Chapter 3, and indicates that the
portunity for trainees to instill rigorous habits and lessons, which will other key components, and their use of the new methods,
serve them well throughout their careers. will be discussed in Chapters 4 and 5.


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

Shortliffe EH. J Am Med Inform Assoc 2016;0:1–4. doi:10.1093/jamia/ocw074, Perspective

innovation or theory that is the main contribution of the work.

Table 1: Organization and components of a generic biomedi- Chapters 4 to n 2 then lay out the subtopics or components that
cal informatics doctoral dissertation. See text for discussion. demonstrate the utility of the innovative contribution. Thus Chapter 3
Typically n is between 7 and 9. 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
Dissertation Key Considerations and Content and then indicates, on the diagram, which elements are covered in
Element which chapter. In Figure 1, as an example, a generic computer system
Title • Play down motivating application that deals with uncertainty modeling in knowledge bases is shown di-
• Play up innovative informatics contribution agrammatically, with components and logical flow shown. In the cor-
responding dissertation’s Chapter 3, the diagram would show what
Abstract • Convey nature of innovative contribution
has been introduced in the current chapter (labeled “uncertainty man-
• Mention motivating application

agement system” and “knowledge base” in the diagram) and then
Summarize validation or evaluation
• Write this summary last, when document is
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
Chapter 1 • Introduction a dissertation that is focused more on social science methods would
• Statement of hypothesis (highlight in bold or be different but ideally would still capture the logical flow of the work
italics) and how the subsequent chapters relate to the total effort.
• Motivation and aims The next to last chapter (Chapter n 1) is typically the evaluation

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• Relevance to biomedicine or health
or demonstration of validity. The nature of this chapter can vary widely
• Overview of research and document

depending on the type of work. The focus is not simply on the motivat-
Road map
ing application but on the effectiveness of the underlying innovative
Chapter 2 • Selective literature review methodology or theory that is the topic of the dissertation.
• Assessment of gaps in prior work Chapter n, then, is the final discussion that summarizes the re-
• Delineation of contributions of dissertation re- sults, the contribution of the work, and the assessment of the initial
search in light of gaps hypothesis, and lays out what lies ahead. A specific discussion of the
Chapter 3 • Presentation of the new idea (method or theory) generalizability of the method and its range of its applicability is to be
in detail encouraged. The author should bear in mind that a reader may have
• Overview of any application developed fully digested only Chapter 1 before reading Chapter n.
• Explanation of Chapters 4 to n 2
• Inclusion of explanatory diagram (Figure 1)
Chapters 4 • Technical presentation of components or The discussion here has necessarily been very general, and individual
to n . 2 subtopics students will need to adapt these guidelines to the specifics of their
own research topic and experimental approach. But the general no-
Chapter n 1 • Evaluation (or demonstration of the validity and/ tions do apply broadly. The effort implied is not wasted. Although only
or impact) of the new idea from Chapter 3 a few dissertations will be published formally as books,7 the lessons

learned in writing one will serve the graduate well, regardless of the
Chapter n • Summary of accomplishments and contributions career path. And much that is written in the document, if not previ-
• Assessment of hypothesis (from Chapter 1) in ously published, can be extracted and adapted for formal publication
light of what has been discussed
in peer-reviewed journals. For example, Chapter 2 is often a great
• Generalizability of the results

source of content that can be edited into an influential review paper
Range of applicability

suitable for publishing.
Future work
• Conclusions
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
in assessing it will be summarized in the final chapter. Chapter 1 be needed, but they depend on scientific advances that need to be
needs to capture readers and bring them into the rest of the docu- well identified and articulated, both in talks and in writing. Everyone in
ment. Still, many readers will focus solely on the first and last chapters both the basic research environment and applied settings will benefit
in the document, and the author needs to bear this in mind when writ- when the scientific base for informatics is strengthened.
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
No competing interests to report.
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 ACKNOWLEDGEMENTS
the literature that are most pertinent to the hypothesis, the anticipated The author gratefully acknowledges the contributions of informatics graduate
contribution of the work, and the alternate approaches and their limita- students over more than 3 decades. The teacher learns from his students, and
tions that the student is attempting to address. much of what is summarized in this article was taught through vibrant interac-
The number of chapters (call it n) in a dissertation will vary, but is tions with doctoral students as they strove to write effective and influential
typically between 7 and 9. Chapter 3 introduces the methodologic dissertations.

Shortliffe EH. J Am Med Inform Assoc 2016;0:1–4. doi:10.1093/jamia/ocw074, Perspective

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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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