Improving the sensitivity of the problem list in an intensive care unit by using natural language processing.
ABSTRACT To improve the completeness of an electronic problem list, we have developed a system using Natural Language Processing to automatically extract potential medical problems from clinical free-text documents; these problems are then proposed for inclusion in an electronic problem list management application. A prospective randomized controlled evaluation of this system in an intensive care unit is reported here. A total of 105 patients were randomly assigned to a control or an intervention group. In the latter, patients had their documents analyzed by the system and medical problems discovered were proposed for inclusion into their problem list. In this population, our system significantly increased the sensitivity of the problem lists, from 8.9% to 41%, and to 77.4% if problems automatically proposed but not acknowledged by users were also considered.
Article: Building a comprehensive clinical information system from components. The approach at Intermountain Health Care.[show abstract] [hide abstract]
ABSTRACT: To discuss the advantages and disadvantages of an interfaced approach to clinical information systems architecture. After many years of internally building almost all components of a hospital clinical information system (HELP) at Intermountain Health Care, we changed our architectural approach as we chose to encompass ambulatory as well as acute care. We now seek to interface applications from a variety of sources (including some that we build ourselves) to a clinical data repository that contains a longitudinal electronic patient record. We have a total of 820 instances of interfaces to 51 different applications. We process nearly 2 million transactions per day via our interface engine and feel that the reliability of the approach is acceptable. Interface costs constitute about four percent of our total information systems budget. The clinical database currently contains records for 1.45 m patients and the response time for a query is 0.19 sec. Based upon our experience with both integrated (monolithic) and interfaced approaches, we conclude that for those with the expertise and resources to do so, the interfaced approach offers an attractive alternative to systems provided by a single vendor. We expect the advantages of this approach to increase as the costs of interfaces are reduced in the future as standards for vocabulary and messaging become increasingly mature and functional.Methods of Information in Medicine 02/2003; 42(1):1-7. · 1.53 Impact Factor
[show abstract] [hide abstract]
ABSTRACT: The electronic problem-oriented medical record was conceived to alleviate limitations of the paper-based medical record, and to improve its organization. The list of medical problems is at the heart of this problem-oriented record, and requires completeness, accuracy and timeliness to fulfill this central role. At Intermountain Health Care (IHC), a problem-oriented electronic medical record is being developed, and features a medical problem list at its core. This list is already in use in the outpatient setting, but is often incomplete, inaccurate and out-of-date. This issue is even more prominent for hospitalized patients. To help maintain a complete, accurate and timely problem list, I developed an Automated Problem List system using Natural Language Processing (NLP) to extract potential medical problems from the patient's electronic clinical documents. These problems are proposed to the user for inclusion in the “official” problem list, along with a link to allow viewing the documents the problem was extracted from. Two main applications compose this system. A background application does all documents processing and analysis using NLP, and the problem list management application allows viewing and editing these proposed problems. In the development of this system, the NLP module of the background application was evaluated first. This laboratory function study showed good recall and satisfying precision; accuracy was further improved by enhancing disambiguation and negation detection. A second study prospectively evaluated the whole Automated Problem List system in a clinical setting at the LDS Hospital. Patients benefiting from this system had more complete and timely problem lists. The sensitivity was higher, and the time between a medical problem's first mention in a clinical document and its addition to the list of problems was significantly reduced. In summary, this dissertation describes the planning, development, implementation and evaluation of a system using NLP to automatically extract medical problems from electronic clinical documents. This Automated Problem List system allowed better quality content of the problem list, opening doors to larger scale use of this system and contributing to possible answers to the challenge of making the problem list a cornerstone of our evolving clinical information system. Doctor of Philosophy;Original: University of Utah Spencer S. Eccles Health Sciences Library (no longer available).
M.D. computing: computers in medical practice 10(2):100-14.
Improving the Sensitivity of the Problem List in an Intensive Care Unit
by Using Natural Language Processing
Stéphane Meystre MD PhDa,b, Peter Haug MDa.
a Department of Medical Informatics, University of Utah, Salt Lake City, Utah, U.S.
b Office Informatique, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
To improve the completeness of an electronic
problem list, we have developed a system using
Natural Language Processing to automatically
extract potential medical problems from clinical free-
text documents; these problems are then proposed for
inclusion in an electronic problem list management
A prospective randomized controlled evaluation of
this system in an intensive care unit is reported here.
A total of 105 patients were randomly assigned to a
control or an intervention group. In the latter,
patients had their documents analyzed by the system
and medical problems discovered were proposed for
inclusion into their problem list. In this population,
our system significantly increased the sensitivity of
the problem lists, from 8.9% to 41%, and to 77.4% if
acknowledged by users were also considered.
The problem-oriented Electronic Health Record
(EHR), centered on the problem list, is seen by many
as a possible answer to the quality of healthcare and
medical errors reduction challenges. At Intermountain
Health Care (IHC; Salt Lake City, Utah), the problem
list is an important piece of the medical record, and a
central component of HELP2, a new clinical
information system in development 1. To enable its
potential benefits, the problem list has to be as
accurate, complete and
Unfortunately, problem lists are usually incomplete
and inaccurate, and are often totally unused. To
address this deficiency, we have created an
application using Natural Language Processing (NLP)
to harvest potential problem list entries from the
multiple free-text electronic documents available in a
patient’s EHR. The medical problems identified are
then proposed to the physicians for addition to the
official problem list2. We hypothesize that the use of
NLP to automatically provide potential medical
problems will improve the completeness of this
Automated Problem List.
proposed but not
timely as possible.
More than three decades after Larry Weed proposed
the Problem-Oriented Medical Record (POMR)3,4 as
an answer to the complexity of the medical
knowledge and clinical data, and to address
weaknesses in the documentation of medical care, the
problem-oriented EHR and the problem list have seen
renewed interest as an organizational tool5-10.
Advantages to this approach are that the problem list
provides a central place for clinicians to obtain a
concise view of all patients’ medical problems, that it
facilitates associating clinical information in the
record to a specific problem, and that it can encourage
an orderly process of clinical problem solving and
clinical judgment. The problem list in a problem–
oriented patient record also provides a context in
which continuity of care is supported, preventing
redundant actions5. The Institute of Medicine11
recommends that the Computer-based Patient Record
contain a problem list that specifies the patient’s
clinical problems and the status of each. Also,
convinced of the benefits of the problem list, the Joint
Commission for the Accreditation of Hospitals
(JCAHO12) has established it as a required feature of
The patient record contains a large amount of
information captured as narrative text. These free-text
documents represent the majority of the information
used for medical care13 but decision-support,
research, and quality improvement create a need for
structured and coded data instead. As a possible
answer to this issue, NLP can be used to convert free-
text into coded data14.
Several groups have evaluated NLP techniques with
medical free-text. Examples are MedLEE (Medical
Language Extraction and Encoding system)15, and
applications developed by our medical informatics
group at the University of Utah: SymText16 and
MPLUS17. Other systems that automatically map
clinical text concepts to standardized vocabularies
have been reported, notably MetaMap18,19. MetaMap,
and its Java™ version called MMTx (MetaMap
Transfers), were developed by the U.S. National
Library of Medicine (NLM). They map concepts in
the analyzed text with UMLS concepts. The mapped
AMIA 2006 Symposium Proceedings Page - 554
concepts are ranked, but no negation detection is
Negation detection is a required feature when
analyzing clinical narrative text where findings and
diseases are often described as absent. To this end,
negation detection algorithms have been developed,
At Intermountain Health Care (IHC), the web-based
clinical information system called HELP21 offers
secured access to clinical data through specialized
modules like “Patient
“Medications”, and “Problems”. The “Problems”
module allows viewing, modifying, and adding
medical problems along with their status (active,
inactive, resolved, or error) and other information.
This electronic problem list was already in use in the
outpatient setting, but was not commonly used for
hospitalized patients. The medical and surgical ICU at
the LDS Hospital in Salt Lake City was piloting the
use of this problem list. This ward participated in our
study. All other inpatient wards were using a paper-
based problem list, or no problem list at all.
Materials and Methods
As mentioned earlier, the Automated Problem List
system uses NLP to extract potential medical
problems from free-text medical documents. The two
main components of the system are a background
application and the problem list management
application. The background application does text
processing and analysis and stores extracted problems
in the central clinical database. These problems can
then be accessed by the problem list management
application integrated into HELP2. The background
application has already been evaluated and has shown
good performance21. During the study described here,
the background application looked for 80 different
diagnosis problems, which were selected based on
their frequency in the clinical environments chosen
for our evaluation (a medical and surgical intensive
care unit). The NLP tools used in this experiment
were based on MMTx with a customized data subset
adapted to our set of 80 targeted medical problems.
The negation detection algorithm used was NegEx in
its latest version called NegEx222. The problem list
“Problems” module described above. It was
enhanced to take advantage of the problems
automatically detected by the background application.
These problems were listed with a new proposed
status, and included a link back to the source
document(s) with sentence(s) the problem was
extracted from highlighted for easier reading.
Study design: In this prospective evaluation of our
Automated Problem List system in a clinical
was based on the
environment, adult patients hospitalized in a medical
and surgical ICU and in cardiovascular surgery (LDS
Hospital, Salt Lake City, Utah) were randomly
assigned to a control or to an intervention group. In
the control group, patients received care from
physicians using the standard electronic problem list
(without proposed problems). In the intervention
group, patients were treated by physicians with access
to the Automated Problem List system. Their
documents were analyzed by the background
application, and medical problems extracted were
proposed for inclusion into their electronic problem
This Randomized Controlled Trial was single
blinded. Users of the problem list were physicians
and could not be blinded, since the difference in
content of the problem list between the two groups
was obvious (intervention patients had proposed
problems). The information used was that routinely
collected as part of the patient work-up, and patients
were not aware of the study.
Reference standard: The reference standard for our
study was created using an electronic chart review.
Two physicians independently reviewed each
electronic document with a web-based review
application. They were asked to detect all mentions of
any of the 80 targeted problems that were present (i.e.
not negated), in the present or in the past. When the
two reviewers disagreed, a third physician determined
the presence or absence of the disputed problem. The
documents analyzed were all clinical documents
(radiology reports, consultation reports, progress
notes, H&Ps, discharge summaries, etc.) stored for
each patient during his hospital stay, plus a maximum
of 5 older documents from previous hospital stays or
outpatient care episodes.
The reviewers also examined the patients’ electronic
problem list. They mapped problems that were
entered as free-text (not
corresponding coded problem, and also mapped
children of our targeted problems to the relevant
parent problem (such as Fallot’s triad mapped with
atrial septal defects).
Problem list completeness: Three different problem
lists were considered for each patient: the reference
standard (i.e. what should have been in the problem
list), the “official” problem list (i.e. problems
recorded in the clinical database as active, inactive, or
resolved), and the “potential” problem list (i.e.
problems included in the “official” list, with the
addition of problems that had not been reviewed and
changed from a proposed status). The content of each
patient’s official and potential problem list was
compared with the reference standard, and each
coded) with the
AMIA 2006 Symposium Proceedings Page - 555
problem list entry was counted and categorized as
true positive (TP; problem present in the patient’s
documents and in the problem list), false negative
(FN; problem documented in the patient’s record but
absent from the problem list), false positive (FP;
problem absent but listed in the problem list), or true
negative (TN; problem absent and not listed in the
We then calculated the sensitivity (TP / TP+FN) for
each patient, and averaged across the group of
Ten different reviewers, all physicians, reviewed
clinical documents to create the reference standard.
Reviewers’ overall agreement was very good, with a
Finn’s R of 0.897 when reviewing documents and
0.995 when reviewing problem lists. Finn’s R was
used instead of Cohen’s kappa, because the
agreement table was strongly skewed, with far more
true negatives than true positives.
Because of lack of usage of the electronic problem
list in the cardiovascular surgery ward during the
study, this experiment and its analysis were focused
on the ICU patients. In this ward, 105 patients were
enrolled, with 54 patients randomly assigned to the
intervention group, and 51 to the control group. A
total of 719 medical problems were automatically
extracted and proposed during the study, and about
half were added to the “official” problem list or
rejected as errors (Fig. 1).
Figure 1: Number and proportion of proposed medical
problems and their subsequent status modifications.
Problem list sensitivity: Mean and 0.95 confidence
intervals were computed (Table 1). Analysis of all
patients from the ICU showed significant differences
between control and intervention groups (Fig. 2).
Patients in the intervention group had a more
complete problem list, with a significantly higher
sensitivity. When analyzing the potential problem list
(i.e. including problems that had remained proposed),
the sensitivity was again significantly higher,
reaching about 77%.
When analyzing the subset of patients with a problem
list that had been edited during their stay in the ICU
(43 of the 105 patients), the sensitivity of their
problem list was also significantly higher in the
Figure 2: Results in ICU patients, in the control and
intervention groups. Results of potential problem lists (i.e.,
with proposed problems) are also displayed.
Statistical analysis was executed using a non-
parametric test (Mann-Whitney test) for non-
This evaluation of our Automated Problem List
system suggests that the addition of NLP to support
completeness was successful. The sensitivity we
measured was significantly increased. Enhancing the
problem list management application with NLP made
the problem list more complete.
The excellent inter-reviewer agreement in this study
allowed us a high quality reference standard. This
was made possible by the use of explicit review
techniques23; the list of targeted problems was always
provided beside the document or problem list to
Our results are difficult to compare to other published
results because only very few such studies have been
published. A rare example is an evaluation by Szeto
et al., measuring the accuracy of an outpatient
problem list for 9 different diagnoses24.
A sensitivity of 49% was measured. Our study
considered 80 different diagnoses, and gave very
similar specificity results, but the sensitivity without
intervention was much lower. The effect of our
Automated Problem List system increased the
sensitivity to a similar degree.
AMIA 2006 Symposium Proceedings Page - 556
Table 1: Measurements during the study, with means and 95% confidence intervals, in all ICU patients and patients
with an edited problem list (Inter+prop corresponds to the potential problem list).
The medical problem list figures prominently in
our plans for computerized physician order entry
and medical documentation in the new HELP2
system currently under development at IHC. A
well-maintained problem list will significantly
enhance these applications.
The Automated Problem List could be beneficial
for many reasons: a better problem list could
potentially improve patient outcomes and reduce
costs by reducing omissions and delays,
improving the organization of care, and reducing
adverse events. It could enhance decision-
support for applications requiring knowledge of
patient medical problems.
Several limitations of our system and of this
study need to be discussed. A first important
issue is the use of the problem list by physicians.
The application suite in which these tools were
embedded originated in the outpatient setting and
is in the process of moving into the hospital
environment. As mentioned in the background
section of this paper, the problem list currently
used in this environment is paper-based and is
usually incomplete and not timely. In fact, it is
often totally unused. There is good reason for
this. None of the therapeutic or documentation
functions that are done by the physicians are
currently tied, in any way to the problem list.
In the electronic record that is evolving at our
institution, the problem list will be integrated
into the care process. Electronic order entry,
documentation, and a variety of decision support
tools will be tied to it. Unfortunately, these
applications either do not currently exist or exist
as limited prototypes. The single function
currently mediated through the problem list is the
“infobutton”25 a tool that provides problem-
specific medical knowledge to the user.
Therefore, this study is best seen as an effort to
explore the possibilities offered by NLP to
support the problem list. Today, encouraging
clinicians to enter data in the problem list and
convincing them of the benefits of the problem
list remains a challenge.
Another issue with this system is the scalability
of the list of targeted medical problems. Our
system is currently designed to extract only 80
different medical problems. Those 80 problems
represented about 64% of all coded medical
problem instances in our EHR in 2003; however,
many more problems will be needed to allow this
system to be used in other settings. A very
simple solution is to use the default full UMLS
data set provided with MMTx instead of a
custom data subset, but this reduces the NLP
module performances: it decreases the recall and
makes it slower.
This work is supported by a Deseret Foundation
Grant (Salt Lake City, Utah). We would like to
thank Min Bowman for her help with the
modified Problems module. We would also like
to thank Greg Gurr for his advices and his help.
Scott Narus and Stan Huff also gave us helpful
advice and guidance for which we are grateful.
Finally, we are especially grateful to Terry
Clemmer whose enthusiasm for the problem list
made this study possible.
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