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<title>Unified Medical Language System (UMLS) (CBM 96-8)</title>
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<H2 id=skipNLMNav>Current Bibliographies in Medicine 96-8</H2><!-- ************************* Content start ************************* -->
<HR>
<H1><A name=list>Unified Medical Language System® (UMLS®)</A> </H1>
<HR>
<P>January 1986 through December 1996</P>
<P>280 Citations</P>
<P>Prepared by <BR>Catherine R. Selden, M.L.S.<BR>Betsy L. Humphreys,
M.L.S.<BR></P>
<P>U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES<BR>Public Health
Service<BR>National Institutes of Health</P>
<P><A "http://www.nlm.nih.gov/nlmhome.html">National Library of
Medicine</A><BR>Reference Section<BR>8600 Rockville Pike<BR>Bethesda,
Maryland 20894</P>
<P>1997</P>
<HR>
<P><STRONG>National Library of Medicine Cataloging in
Publication</STRONG></P>
<P>Selden, Catherine <BR>Unified Medical Language System (UMLS): January
1986 through December 1996 : 280 citations / prepared by Catherine R.
Selden, Betsy L. Humphreys. -- Bethesda, Md. (8600 Rockville Pike,
Bethesda 20894) : U.S. Dept. of Health and Human Services, Public Health
Service, National Institutes of Health, National Library of Medicine,
Reference Section ; Pittsburgh, PA : Sold by the Supt. of Docs., U.S.
G.P.O., 1997.<BR>-- (Current bibliographies in medicine ; 96-8)</P>
<P>1. Unified Medical Language System - bibliography 2. Vocabulary,
Controlled - bibliography 3. Natural Language Processing - bibliography I.
Humphreys, Betsy L. II. National Library of Medicine (U.S.). Reference
Section III. Title IV. Series</P>
<P>02NLM: ZW 1 N272 no. 96-8</P>
<HR>
<H2>Contents</H2>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#12">Series
Note</A></H3>
<H3><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#8">Foreword</A></H3>
<H3><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#10">Introduction</A></H3>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#18">Search
Strategy</A></H3>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#20">Sample
Citations</A></H3>
<H3><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#15">Bibliography</A></H3><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A>
<HR>
<P><A name=12><STRONG>Series Note</STRONG></A></P>
<P>Current Bibliographies in Medicine (CBM) is a continuation in part of
the National Library of Medicine's Literature Search Series, which ceased
in 1987 with No. 87-15. In 1989 it also subsumed the Specialized
Bibliography Series. Each bibliography in the new series covers a distinct
subject area of biomedicine and is intended to fulfill a current awareness
function. Citations are usually derived from searching a variety of online
databases. Citations are usually derived from searching a variety of
online databases. <A
"http://www.nlm.nih.gov/pubs/factsheets/online_databases.html">NLM
databases</A> utilized include MEDLINE®, AVLINE®, BIOETHICSLINE®,
CANCERLIT®, CATLINE®, HEALTHSTAR<SUP><FONT size=1>tm</FONT></SUP>,
POPLINE<SUP><FONT size=1>tm</FONT></SUP> and TOXLINE®. The only criterion
for the inclusion of a particular published work is its relevance to the
topic being presented; the format, ownership, or location of the material
is not considered. </P>
<P>Comments and suggestions on this series may be addressed to:</P>
<P>Karen Patrias, Editor<BR>Current Bibliographies in
Medicine<BR>Reference Section<BR>National Library of Medicine<BR>Bethesda,
MD 20894<BR>Phone: 301-496-6097<BR>Fax: 301-402-1384<BR><A
"mailto:ref@nlm.nih.gov">mailto:ref@nlm.nih.gov</A></P>
<P>This bibliography, CBM 96-8, is the last publication in this series for
calendar year 1996.</P>
<P>Ordering Information:</P>
<P><EM>Current Bibliographies in Medicine</EM> is sold by the
Superintendent of Documents, U.S. Government Printing Office, P.O. 371954,
Pittsburgh, PA 15250-7954. Orders for individual bibliographies in the
series ($5.50, $6.88 foreign) should be sent to the Superintendent of
Documents citing the title, CBM number, and the GPO List ID number.</P>
<P>Internet Access:</P>
<P>The <EM>Current Bibliographies in Medicine</EM> series is also
available at no cost to anyone with Internet access through the Library's
World Wide Web site at <A
"http://www.nlm.nih.gov/pubs/resources.html">http://www.nlm.nih.gov/pubs/resources.html</A>.</P>
<P>Use of funds for printing this periodical has been approved by the
Director of the Office of Management and Budget through September 30,
1997.</P><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A> | <A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#15">Return to table of
contents</A>
<HR>
<P><STRONG><A name=8>FOREWORD</A></STRONG> </P>
<P>This bibliography marks the tenth anniversary of the National Library
of Medicine's Unified Medical Language System® (UMLS®) project, a
long-term research and development effort with the ambitious goal of
enabling computer systems to "understand" medical meaning. The project was
proposed to Congress as essential to the development of advanced health
information systems -- and as requiring an initial 5-10 year development
phase which would cost $1-3 million per year. The Congress responded with
generous and faithful support. </P>
<P>In 1986, we foresaw a future with widespread access to more powerful,
less expensive computers, improved telecommunications, and a huge array of
diverse machine-readable biomedical information sources. In such a future,
health professionals and researchers would be able to obtain information
relevant to practice or research decisions when and where needed -- but
only if automated systems could interpret their inquiries correctly,
identify databases likely to have information relevant to these inquiries,
and retrieve the pertinent information from those sources. The UMLS
project set out to design and build Knowledge Sources that could be used
by computer programs to overcome the barriers to effective information
retrieval caused by disparities in language and by the scattering of
information across many databases and systems. We understood from the
beginning that designing and building the Knowledge Sources would in fact
be easier and less expensive than maintaining them over time in order to
reflect new biomedical discoveries and concepts. For this reason, an
institution like NLM was considered to be more appropriate for directing
the UMLS project than a university department operating under short-term
grant support. </P>
<P>Ten years later our predictions regarding computers, communications,
and biomedical databases have proven to be roughly accurate, and the
explosive growth of the Internet and the World-Wide Web has both
simplified and magnified the problems the UMLS is designed to address. NLM
has issued annual editions of the UMLS Knowledge Sources since 1990 and,
in 1996, sent them to more than 700 system developers around the world.
Use of the UMLS Knowledge Sources allows many different computer systems,
including NLM's own Internet Grateful Med, to behave as if they had at
least a limited understanding of the medical meaning in words and phrases
used by questioners. Interest in controlling the language used in
computer-based patient records, as an aid to decision support, quality
control, and research, has spread from the medical informatics community
to those delivering and paying for health care. In this environment, there
is increasing interest in applying the UMLS products. </P>
<P>A long-term project of the breadth and complexity of the UMLS requires
a team with knowledge and skills from many fields. From its inception, the
UMLS effort has involved internal research and development by NLM staff,
competitively awarded contracts and grants for research assistance from
many U.S. informatics research groups, and volunteer UMLS users worldwide,
who have tested the Knowledge Sources in different environments and
provided valuable suggestions for their improvement. The UMLS project is
also indebted to the producers of many important biomedical vocabularies
and classifications who provided their terminologies to NLM for
incorporation in the UMLS Metathesaurus. </P>
<P>Set out below are the research groups and principal investigators who
have been NLM's major partners in developing and testing the UMLS
Knowledge Sources:</P>
<UL>
<LI>Beth Israel Hospital, Charles Safran, M.D.<BR>
<LI>Brigham &amp; Women's Hospital, Robert A. Greenes, M.D., Ph.D.
<LI>Carnegie-Mellon University, David A. Evans, Ph.D.
<LI>Columbia University, James J. Cimino, M.D.
<LI>Indiana University, Clement J. McDonald, M.D.
<LI>Kaiser Permanente, Simon Cohn, M.D., M.P.H.
<LI>Lexical Technology, Inc., Mark S. Tuttle
<LI>Massachusetts General Hospital, G. Octo Barnett, M.D.
<LI>Mayo Foundation, Christopher G. Chute, M.D., Ph.D.
<LI>Oregon Health Sciences University, William R. Hersh, M.D.
<LI>University of California, San Francisco, Marsden S. Blois, M.D.,
Ph.D.
<LI>University of Pittsburgh, Randolph A. Miller, M.D., Gregory F.
Cooper, M.D., Ph.D., Henry J. Lowe, M.D.
<LI>University of Utah, Homer R. Warner, M.D., Ph.D.
<LI>Yale School of Medicine, Perry L. Miller, M.D., Ph.D. </LI></UL>
<P>Literally dozens of individuals from these and other institutions have
made substantial contributions to the UMLS project. We thank them all for
what has been a gratifying and productive association. </P>
<P>The UMLS has benefited from the talent, energy, and insight of many
leaders in medical informatics and medical librarianship, most of whom are
well-represented in this bibliography. One scientist whose number of UMLS
publications does not adequately reflect his importance to the project is
Marsden Scott Blois, M.D., Ph.D. Dr. Blois was awarded one of the first
UMLS research contracts in 1986; he died in 1988 just after the project's
exploratory phase concluded. His seminal thinking about medical
information [1,2] greatly influenced the UMLS project and the design of
the UMLS Metathesaurus. His NLM colleagues and friends believe that, like
us, he would have been pleased -- but not satisfied -- with the UMLS
achievements of the past decade. </P>
<P>Donald A.B. Lindberg, M.D.<BR>Director, National Library of
Medicine<BR></P>
<P>Betsy L. Humphreys, M.L.S.<BR>Assistant Director for Health Services
Research Information, National Library of Medicine <BR></P>
<P><CITE>1. Blois MS. Information and medicine: the nature of medical
descriptions. Berkeley: University of California Press;
1984.</CITE><BR><CITE>2. Blois MS. Medicine and the nature of vertical
reasoning. N Engl J Med 1988 Mar 31;318(13):847-51.</CITE> </P><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A> | <A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#15">Return to table of
contents</A><BR>
<HR>
<P><STRONG><A name=10>INTRODUCTION</A></STRONG></P>
<P>Unified Medical Language System</P>
<P>In 1986, the National Library of Medicine (NLM) began a long-term
research and development project to build the Unified Medical Language
System (UMLS®). The purpose of the UMLS is to aid the development of
systems that help health professionals and researchers retrieve and
integrate electronic biomedical information from a variety of sources. The
UMLS approach involves the development of machine-readable Knowledge
Sources that can be used by a wide variety of applications programs to
compensate for differences in the way concepts are expressed in different
machine-readable sources and by different users, to identify the
information sources most relevant to a user inquiry, and to negotiate the
telecommunications and search procedures necessary to retrieve information
from these sources. The goal is to make it easy for users to link
disparate information systems, including computer-based patient records,
bibliographic databases, factual databases, and expert systems. </P>
<P>The UMLS project is directed by a multi-disciplinary team of NLM staff
and involves medical informatics research groups across the United States
working under competitively awarded contracts and grants. More than 700
volunteer users receive the annual editions of the UMLS products free of
charge under the terms of a license agreement. The Knowledge Sources are
iteratively refined and expanded based on feedback from those applying
each successive version. </P>
<P>There are four UMLS Knowledge Sources: the Metathesaurus®:, the
SPECIALIST<SUP><FONT size=1>tm</FONT></SUP> Lexicon, a Semantic Network
and an Information Sources Map. Most heavily used to date, the
Metathesaurus provides a uniform, integrated distribution format for more
than 30 biomedical vocabularies and classifications, linking many
different names for the same concepts. The Lexicon contains syntactic
information for many Metathesaurus terms, component words, and English
words, including verbs, that do not appear in the Metathesaurus. The
Semantic Network contains information about the types or categories (e.g.,
"Disease or Syndrome," "Virus") to which all Metathesaurus concepts have
been assigned and the permissible relationships among these types (e.g.,
"Virus" causes "Disease or Syndrome"). The Information Sources Map or
directory contains both human-readable and machine-"processable"
information about the scope, location, vocabulary, syntax rules, and
access conditions of biomedical databases of all kinds. The references in
this bibliography cover the structure and semantics of the UMLS Knowledge
Sources, their development and maintenance, and assessments of their
coverage and utility for particular purposes. Some of this literature
reflects understandable confusion about the relationship of the
Metathesaurus to its constituent vocabularies. </P>
<P>The UMLS Knowledge Sources were designed as multi-purpose tools, to
facilitate the development of more effective biomedical information
systems. As intended, they have been applied in a wide variety of research
and development environments to many different tasks, including vocabulary
development, knowledge representation, clinical data capture, linking
patient data to knowledge sources, curriculum analysis, natural language
processing, automated indexing, and information retrieval. This
bibliography covers the full range of UMLS applications. </P>
<P>Particularly in its early years, but also more recently, the UMLS
project commissioned exploratory and ancillary studies on such topics as
user information needs, methods of organizing and merging vocabulary
information, and information retrieval techniques and also developed
specialized tools for use in the research effort. The bibliography also
includes published articles describing these efforts. </P>
<P>NLM staff members and outside observers have viewed the UMLS project as
an important complement to other initiatives affecting access to
information and information technology, including Integrated Advanced
Information Management Systems (IAIMS), the High Performance Computing and
Communications Program, and the emerging National Information
Infrastructure. Some commentators have been critical of the UMLS's purpose
and its approach. The bibliography includes discussions of the
relationship of the UMLS to other programs as well as commentaries on its
potential value. </P>
<P>The references in this bibliography include journal articles, book
chapters, technical reports, dissertations, and conference papers that
include substantive discussions of the UMLS project, the UMLS Knowledge
Sources, UMLS applications, and related studies carried out under the
auspices of the UMLS project. In general, meeting abstracts, letters,
comments, and editorials are included only if they present research
findings or express opinions about the project not reflected elsewhere.
Although both English and foreign language publications are cited, most
references are to English language publications. References are arranged
by subject and appear under only one topic. Abstracts have been included
if permission was granted by copyright holders. Special copyright notices
appear at the end of the abstracts if requested by copyright holders. </P>
<P>The compilers wish to thank Marlyn Schepartz, National Library of
Medicine, for her expert production and editorial assistance; Alexa T.
McCray, Ph.D. for help in organizing the references; and the many UMLS
researchers who reviewed an early draft of the bibliography and provided
additional relevant references. </P><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A> | <A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#15">Return to table of
contents</A>
<HR>
<P><A name=18><STRONG>Search Strategy</STRONG></A></P>
<P>A variety of online databases are usually searched in preparing
bibliographies in the CBM series. To assist you in updating or otherwise
manipulating the material in this search, the strategy used for the NLM's
MEDLINE database is given below. Please note that the search strategies
presented here differ from individual demand searches in that they a re
generally broadly formulated and irrelevant citations edited out prior to
printing.</P>
<P>SS1 = UNIFIED MEDICAL LANGUAGE SYSTEM OR VOCABULARY, CONTROLLED
OR<BR>NATURAL LANGUAGE PROCESSING<BR>SS2 = (TW) UNIFIED AND MEDICAL AND
LANGUAGE AND SYSTEM OR UMLS<BR>SS3 = (TW) NATURAL AND LANGUAGE AND
PROCESSING OR METATHESAURUS<BR>SS4 = SEMANTIC@NETWORK<BR>SS5 =
KNOWLEDGE@SOURCES#<BR>SS6 = INFORMATION@SOURCES@MAP<BR>SS7 = 1 OR 2 OR 3
OR 4 OR 5 OR 6 <BR></P>
<P><STRONG>GRATEFUL MED and INTERNET GRATEFUL MED</STRONG></P>
<P>To make online searching easier and more efficient, the Library offers
GRATEFUL MED, microcomputer-based software that provides a user-friendly
interface to most NLM databases. This software was specifically developed
for health professionals and features multiple choice menus and "fill in
the blank" screens for easy search preparation. GRATEFUL MED runs on an
IBM PC (or IBM-compatible) with DOS 2.0 or Windows or on a Macintosh, and
requires a Hayes (or Hayes-compatible) modem. It may be purchased from the
National Technical Information Service in Springfield, Virginia, for
$29.95 (plus $3.00 per order for shipping). For your convenience, an order
blank has been enclosed at the back of this bibliography.</P>
<P>INTERNET GRATEFUL MED is available from the World Wide Web. The user
with Internet access and an NLM user account need only point a compatible
Web browser (Netscape Navigator is strongly recommended) to <A
"http://igm.nlm.nih.gov/">http://igm.nlm.nih.gov/</A>. No other
software at the user end is required.</P><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A> | <A
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contents</A>
<HR>
<P><STRONG><A name=20>Sample Citations</A></STRONG> </P>
<P>Citations are formatted according to the rules established for
<EM>Index Medicus</EM> ®. Sample journal and monograph citations appear
below. For journal articles written in a foreign language, the English
translation of the title is placed in brackets; for monographs, the title
is given in the original language. In both cases the language of
publication is shown by a three letter abbreviation appearing at the end
of the citation.</P>
<P><STRONG>Journal Article:</STRONG></P>
<P><EM>Example:</EM><BR>Cimino JJ. Use of the Unified Medical Language
System in patient care at the Columbia-Presbyterian Medical Center.
Methods Inf Med 1995 Mar;34(1-2):158-64. </P>
<P><EM>Order, with separating punctuation:</EM><BR>Authors. Article Title.
Abbreviated Journal Title Date;Volume(Issue):Pages.</P>
<P><STRONG>Book Chapter:</STRONG></P>
<P><EM>Example:</EM><BR>McCray AT. Representing biomedical knowledge in
the UMLS semantic network. In: Broering NC, editor. High-performance
medical libraries: advances in information management for the virtual era.
Westport (CT): Meckler; 1993. p. 31-44. </P>
<P><EM>Order, with separating punctuation:</EM><BR>Chapter Authors.
Chapter Title. Book Editor. Book Title. Place of Publication: Publisher;
Date. Pages.</P>
<P>For details of the formats used for references, see the following
publication:<BR>Patrias, Karen. <EM>National Library of Medicine
recommended formats for bibliographic citation</EM>. Bethesda (MD): The
Library; 1991 Apr. Available from: NTIS, Springfield, VA; PB91-182030.
</P><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to
title page</A> | <A
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contents</A>
<HR>
<H2><A name=15>TABLE OF CONTENTS FOR UMLS CBM</A></H2>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#1">Overview and
Conceptual Foundations</A></H3>
<H3>UMLS Knowledge Sources</H3>
<UL>
<LI>Metathesaurus and Semantic Network<BR>
<UL>
<LI><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#2a">-Structural and
Semantic Properties</A><BR>
<LI><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#2b">-Development
and Maintenance</A><BR>
<LI>-<A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#2c">Content
Coverage</A><BR></LI></UL>
<LI><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#2d">Information
Sources Map</A><BR>
<LI><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#2e">Distribution
Formats and Associated Tools</A><BR></LI></UL>
<H3>UMLS Applications</H3>
<UL>
<LI>Vocabulary Construction and Concept Discovery<BR>
<UL>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3a">-
Vocabulary Design, Construction, and Maintenance</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3b">-
Vocabulary Standards, Servers, and Mapping Methods</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3c">-
Knowledge Acquisition and Concept Discovery</A><BR></LI></UL>
<LI>Data Creation<BR>
<UL>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3d">-
Clinical Data</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3e">-
Curricula and Faculty Interests</A><BR></LI></UL>
<LI>Natural Language processing, Indexing, and Retrieval<BR>
<UL>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3f">- NLP
Methods and Algorithms</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3g">-
Indexing and Retrieval Methods and Algorithms</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3h">-
Information Retrieval Systems</A><BR></LI></UL>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3i">Linking
Clinical Systems to Knowledge-Based Information Sources</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#3j">Access to
Multiple Knowledge-Based Information Sources</A><BR></LI></UL>
<H3>Preliminary and Ancillary Studies</H3><BR>
<UL>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4a">User
Information Needs</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4b">Vocabulary
Analysis and Merging</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4c">Knowledge
Acquisition and Representation</A><BR>
<LI><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4d">Information and
Retrieval Techniques</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4e">Vocabulary
Browsers</A><BR>
<LI><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#4f">Research
Tools</A><BR></LI></UL>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#5">The UMLS in
Relation to Other Programs</A></H3>
<H3><A href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#6">Commentaries
and Opinions about UMLS</A></H3><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
page</A>
<HR>
<H3><A name=1>Overview and Conceptual Foundations</A></H3>
<HR>
<P>Hattery M. UMLS: guide and translator in the land of medical research.
Inf Retr Libr Autom (US) 1992 Feb;27(9):1-6.</P>
<P>Humphreys BL, Lindberg DA. Building the Unified Medical Language
System. Proc Annu Symp Comput Appl Med Care 1989:475-80. The National
Library of Medicine's Unified Medical Language System (UMLS) project has
moved from a period of background studies and exploration of alternatives
to the actual construction of the first versions of important UMLS
components. This paper discusses the UMLS development strategy and
assumptions, describes briefly the UMLS components as currently
envisioned, and then focuses on the content of the first version of the
UMLS metathesaurus (Meta-1), its central vocabulary component. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Humphreys BL, Lindberg DA. The UMLS project: making the conceptual
connection between users and the information they need. Bull Med Libr
Assoc 1993 Apr;81(2):170-7. Conceptual connections between users and
information sources depend on an accurate representation of the content of
available information sources, an accurate representation of specific user
information needs, and the ability to match the two. Establishing such
connections is a principal function of medical librarians. The goal of the
National Library of Medicine's Unified Medical Language System (UMLS)
project is to facilitate the development of conceptual connections between
users and relevant machine-readable information. The UMLS model involves a
combination of three centrally developed Knowledge Sources (a
Metathesaurus, a Semantic Network, and an Information Sources Map) and a
variety of smart interface programs that make use of these Knowledge
Sources to help users in different environments find machine-readable
information relevant to their particular practice or research problems.
The third experimental edition of the UMLS Knowledge Sources was issued in
the fall of 1992. Current priorities for the UMLS project include
developing applications that make use of the Knowledge Sources and using
feedback from these applications to guide ongoing enhancement and
expansion of the Knowledge Sources. Medical librarians are involved
heavily in the direction of the UMLS project, in the development of the
Knowledge Sources, and in their experimental application. The involvement
of librarians in reviewing, testing, and providing feedback on UMLS
products will increase the likelihood that the UMLS project will achieve
its goal of improving access to machine-readable biomedical information.
Copyright by and reprinted with permission of the Medical Library
Association.</P>
<P>Humphreys BL, Lindberg DA. The Unified Medical Language System project:
a distributed experiment in improving access to biomedical information.
Medinfo 1992;7(Pt 2):1496-500. The goal of the US National Library of
Medicine's UMLS project is to overcome the barriers to information access
caused by the variety of ways the same biomedical concepts are expressed
and by the fragmentation of useful biomedical information among disparate
databases and systems. The UMLS strategy focuses on the development of new
knowledge sources that can be used by a variety of intelligent programs to
compensate for differences in the terminology employed by users and
information sources and in database structure and content. The early
versions of the UMLS Knowledge Sources are intended for use by system
developers. They are available free of charge under the terms of an
experimental agreement and have been distributed to 150 sites throughout
the world. Priorities for annual enhancement to the UMLS components will
be based on feedback received from those who are applying these new tools
to a variety of information access problems.</P>
<P>Humphreys BL, Lindberg DA, Hole WT. Assessing and enhancing the value
of the UMLS Knowledge Sources. Proc Annu Symp Comput Appl Med Care
1991:78-82. The goal of the UMLS Project is to give practitioners and
researchers easy access to machine-readable information from diverse
sources. Assessment of the first experimental versions of the UMLS
Knowledge Sources is essential to measuring progress toward that goal and
to identifying needed enhancements. As of July 30, 1991, copies of the
first edition of the UMLS Knowledge Sources had been distributed to 143
individuals and institutions; 66 had provided initial feedback
information. The information received indicates that the UMLS Knowledge
Sources will undergo broad testing in the patient care, medical education,
library service, and product development environments. Preliminary data
support the hypothesis that expanded coverage of routine clinical concepts
is needed. Key enhancements planned for 1992 and beyond include expanded
coverage of ICD-9-CM and CPT. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Humphreys BL, Schuyler PL. The Unified medical language system: Moving
beyond the vocabulary of bibliographic retrieval. In: Broering NC.,
editor. High-performance medical libraries: advances in information
management for the virtual era. Westport (CT): Meckler; 1993. p. 31-44.
The National Library of Medicine's (NLM) Medical Subject Headings (MeSH)
is an extensive biomedical thesaurus used to index, catalog, and retrieve
citations to the biomedical literature. It is one of a number of source
vocabular ies for the Unified Medical Language System (UMLS), a major NLM
research and development program designed to help users to retrieve and
integrate information from a variety of disparate information sources. The
information sources of interest include bibl iographic databases, patient
records systems, factual databanks, and knowledge bases. The UMLS project
has produced three new Knowledge Sources: a Metathesaurus of concepts and
terms from vocabularies and classifications used in different types of
biomedi cal information sources: a Semantic Network of sensible
relationships among the broad semantic types or categories to which all
Metathesaurus concepts are assigned; and an information Sources Map that
describes the scope, content, and access conditions fo r publicly
available biomedical information sources. The UMLS Knowledge Sources are
intended for use by system developers and can be accessed by a variety of
interface programs to interpret user inquiries, identify sources of
information relevant to these queries, and retrieve the relevant
information. A number of specific projects are underway to assess the
usefulness of the current versions of the UMLS Knowledge Sources and to
provide feedback that can guide their future development.</P>
<P>Lindberg DA, Humphreys BL. Computer systems that understand medical
meaning. In: Scherrer JR, Cote RA, Mandil SH, editors, Computerized
natural medical language processing for knowledge representation.
Proceedings of the IFIP-IMIA WG6 International Wo rking Conference; 1988
Sep 12-15; Geneva, Switzerland. Amsterdam: North-Holland; 1989. p. 5-17.
The National Library of Medicine has begun the development of the Unified
Medical Language System (UMLS). The UMLS project is an effort to build an
increasing ly intelligent automated system that understands biomedical
terms and their interrelationships and uses this understanding to help
users retrieve and organize information from machine-readable sources.
Compared to many other efforts to build systems that understand medical
meaning, the UMLS emphasizes breadth of scope, even at the sacrifice of
depth of understanding. To some degree, it must attempt to encompass all
of biomedicine and to provide access to many different types of automated
information. This great breadth is partially offset by the defined and, in
a sense, limited purpose of the UMLS project. The goal of the UMLS is to
facilitate the retrieval and integration of information from a variety of
machine-readable information sources, including de scriptions of the
biomedical literature, clinical records, factual databanks and medical
knowledge bases. The UMLS will compensate for the differences in the
terminologies used in these disparate systems and for variations in the
language employed by user s themselves. </P>
<P>Lindberg DA, Humphreys BL. Toward a unified medical language. In: EFMI
- European Federation for Medical Informatics. Medical Informatics Europe
'87. Proceedings of the 7th International Congress; 1987 Sep 21-25; Rome,
Italy. Rome: Luigi Pozzi; 1987 . p. 23-31.</P>
<P>Lindberg DA, Humphreys BL. The UMLS knowledge sources: tools for
building better user interfaces. Proc Annu Symp Comput Appl Med Care
1990:121-5. The current focus of the National Library of Medicine's
Unified Medical Language System (UMLS) project is the development,
testing, and evaluation of the first versions of three new knowledge
sources: the Metathesaurus, the Semantic Network, and the Information
Sources Map. These three knowledge sources can be used by interface
programs to conduct an intellig ent interaction with the user and to make
the conceptual link between the user's question and relevant machine
readable information. NLM is providing experimental copies of the initial
versions of the UMLS knowledge sources in exchange for feedback on way s
they can and should be improved. The hope is that the results of such
experimentation will provide both immediate improvements in biomedical
information service and useful suggestions for enhancements to the UMLS.
Copyright by and reprinted with permiss ion of the American Medical
Informatics Association.</P>
<P>Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language
System. Methods Inf Med 1993 Aug;32(4):281-91. In 1986, the National
Library of Medicine began a long-term research and development project to
build the Unified Medical Language System (UMLS). The purpose of the UMLS
is to improve the ability of computer programs to understand the
biomedical meaning in user inquiries and to use this understanding to
retrieve and integrate relevant machine-readable information for users.
Underlying the U MLS effort is the assumption that timely access to
accurate and up-to-date information will improve decision making and
ultimately the quality of patient care and research. The development of
the UMLS is a distributed national experiment with a strong ele ment of
international collaboration. The general strategy is to develop UMLS
components through a series of successive approximations of the
capabilities ultimately desired. Three experimental Knowledge Sources, the
Metathesaurus, the Semantic Network, an d the Information Sources Map have
been developed and are distributed annually to interested researchers,
many of whom have tested and evaluated them in a range of applications.
The UMLS project and current developments in high-speed, high-capacity
intern ational networks are converging in ways that have great potential
for enhancing access to biomedical information.</P>
<P>Paterson G. UMLS knowledge sources and Canada: an overview. Bibl Medica
Can 1996 Spring;17(3):102-4.</P>
<P>Schuyler P. Integrated access to medical and pharmacological
information: the unified medical language system at the National Library
of Medicine. In: Proceedings: 1990 International Chemical Information
Conference; Montreux, Switzerland: New York: Springer-Verlag; 1990. p.
195-203.</P>
<P>Squires SJ. Access to biomedical information: the unified medical
language system. Libr Trends 1993 Summer;42(1):127-52. The National
Library of Medicine (NLM) is engaged in a long-term project to develop a
Unified Medical Language System (UMLS) that will retrieve and integrate
information from a variety of information resources. Two UMLS components
use fundamental aspects of controlled vocabulary structure and management
and their relationship to information retrieval that have general interest
for librarianship. The UMLS project is described, along with its initial
deployment in retrieval environments. Reprinted with permission from
Library Trends. Copyright 1993 The Board of Trustees of the University of
Illinois.</P><A
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contents</A>
<HR>
<H3>UMLS Knowledge Sources</H3>
<UL>
<LI><STRONG>Metathesaurus and Semantic Network</STRONG><BR>
<UL>
<LI><STRONG><A name=2a>Structural and Semantic
Properties</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Joubert M, Miton F, Fieschi M, Robert JJ. A conceptual graphs modeling
of UMLS components. Medinfo 1995;8(Pt 1):90-4. The Unified Medical
Language System (UMLS) of the U.S. National Library of Medicine is a
complex collection of terms, concepts, and relationships derived from
standard classifications. Potential applications would benefit from a high
level representation of its components. This paper proposes a conceptual
representation of both the Metathesaurus and the Semantic Network of the
UMLS based on conceptual graphs. It shows that the addition of a
dictionary of concepts to the UMLS knowledge base allows the capability to
exploit it pertinently. This dictionary defines more precisely the core
concepts and adds constraints on their use. Constraints are dedicated to
guide an intelligent browsing of the UMLS knowledge sources.</P>
<P>Lipow SS, Campbell KE, Olson NE, Tuttle MS, Erlbaum MS, Fuller LF,
Sherertz DS, Nelson SJ, Cole WG. Formal properties of the metathesaurus:
An update. Proc Annu Symp Comput Appl Med Care 1995:944.</P>
<P>McCray AT. Representing biomedical knowledge in the UMLS semantic
network. In: Broering NC., editor. High-performance medical libraries:
advances in information management for the virtual era. Westport (CT):
Meckler; 1993. p. 45-55. The Unified Medical Language System (UMLS)
Semantic Network is one of three Knowledge Sources currently available as
part of the National Library of Medicine's (NLM) UMLS Project. The purpose
of the Network is to provide a consistent categorization of all concepts
found in the Metathesaurus and to provide useful links between these
concepts at the level of the semantic types. The Semantic Network is
closely tied to the other two UMLS Knowledge Sources, the Metathesaurus
and the Information Sources Map. Taken together, these three Knowledge
Sources provide powerful tools for enhancing biomedical information
retrieval.</P>
<P>McCray AT. UMLS semantic network. Proc Annu Symp Comput Appl Med Care
1989:503-7. The UMLS network of semantic types is one component of NLM's
evolving Unified Medical Language System. This paper discusses the role of
the semantic network in the overall system, then describes the evolution
and current status of the network, and finally, concludes with a
discussion of plans for further development. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>McCray AT, Hole WT. The scope and structure of the first version of the
UMLS Semantic Network. Proc Annu Symp Comput Appl Med Care 1990:126-30.
The authors discuss the UMLS Semantic Network, one of three UMLS knowledge
sources currently under development by the National Library of Medicine.
They describe the structure and content of the network, and discuss the
relationship between the network and the first version of the UMLS
Metathesaurus. They address the assumptions and process involved in
assigning semantic types to Metathesaurus concepts and conclude with a
description of the distribution format of this knowledge source. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P>
<P>McCray AT, Nelson SJ. The representation of meaning in the UMLS.
Methods Inf Med 1995 Mar;34(1-2):193-201. The UMLS knowledge sources
provide detailed information about biomedical naming systems and
databases. The Metathesaurus contains biomedical terminology from an
increasing number of biomedical thesauri, and the Semantic Network
provides a structure that encompasses and unifies the thesauri that are
included in the Metathesaurus. This paper addresses some fundamental
principles underlying the design and development of the Metathesaurus and
Semantic Network. It begins with a description of the formal properties of
the semantic network. It continues with consideration of the principle of
semantic locality and how this is reflected in the UMLS knowledge sources.
The paper concludes with a discussion of the issues involved in attempting
to reuse knowledge and the potential for reuse of the UMLS knowledge
sources.</P>
<P>Nelson SJ, Fuller LF, Erlbaum MS, Tuttle MS, Sherertz DD, Olson NE. The
semantic structure of the UMLS Metathesaurus. Proc Annu Symp Comput Appl
Med Care 1992:649-53. Meta-1.1, the UMLS metathesaurus, represents medical
knowledge in the forms of names of concepts and links between those
concepts. The representations of the semantic neighborhood of a concept
can be thought of as dimensions of the property of semantic locality and
include term information (broader, narrower, or otherwise related), the co
ntextual information (parent-child, siblings in a hierarchy), the semantic
types, and the co-occurrence data (links discovered empirically from
concepts used to index the medical literature.) The degree of redundancy
of each of these dimensions was invest igated by reviewing the extent of
multiple presentations of concepts which appear as related to a given
concept. The degree of overlap was surprisingly small. While the
co-occurrence data finds some of the links represented by other
dimensions, those link s are but minute fractions of the vast amount of
co-occurrence derived links. Because parent-child relationships are often
subsumptive (or categorical) in nature, it might be expected that siblings
usually share the same semantic types. While true in the aggregate, the
wide variance in percent of types shared may reflect the intended usages
of the source vocabularies. Noun phrases were extracted from the
definitions of 40 concepts in Meta-1 in order to assess systematically the
coverage of important conce pts by Meta-1, and to assess whether the links
between these definitional concepts, which may have special value, and the
concept being defined were indeed present. Out of 161 of these
definitional concepts, 29 were not represented in Meta-1, and 37 of th ose
represented in Meta-1 had no direct link to the concept they were
defining. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Nelson SJ, Tuttle MS, Cole WG, Sherertz DD, Sperzel WD, Erlbaum MS,
Fuller LL, Olson NE. From meaning to term: semantic locality in the UMLS
Metathesaurus. Proc Annu Symp Comput Appl Med Care 1991:209-13. The
Unified Medical Language System Metathesaurus represents the results of a
synthesis of existing biomedical naming systems (thesauri). The naming and
other information about the meanings in the Metathesaurus can be used to
find the preferred naming of that meaning in the source chosen by the
user, by exploiting the property of semantic locality. The aspects of
semantic locality in the Metathesaurus which can be thus exploited are the
terms, the semantic types, the use of that term in a source context, and
the co-occurrence of terms in MEDLINE. To find how a meaning is named in
the source of choice, a user must exploit one of these aspects of semantic
locality, entering a term somehow related to the term being sought, and
navigating to the preferred term. While the first three of these aspects
of semantic locality are normative, the last is empirical. Testing of the
utility of the aspects of semantic locality in information retrieval would
require a uniform interface with 1, no Metathesaurus, 2, the Metathesaurus
without the aspects in question, and 3, the Metathesaurus including all
the aspects. Other potential uses of empirically derived semantic locality
include defining or suggesting potentially relevant concepts in a given
situation. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Schuyler PL, Hole WT, Tuttle MS, Sherertz DD. The UMLS Metathesaurus:
representing different views of biomedical concepts. Bull Med Libr Assoc
1993 Apr;81(2):217-22. The UMLS Metathesaurus is a compilation of names,
relationships, and associated information from a variety of biomedical
naming systems representing different views of biomedical practice or
research. The Metathesaurus is organized by meaning, and the fundamental
unit in the Metathesaurus is the concept. Differing names for a biomedical
meaning are linked in a single Metathesaurus concept. Extensive additional
information describing semantic characteristics, occurrence in
machine-readable information sources, and how concepts co-occur in these
sources is also provided, enabling a greater comprehension of the concept
in its various contexts. The Metathesaurus is not a standardized
vocabulary; it is a tool for maximizing the usefulness of existing
vocabularies. It serves as a knowledge source for developers of biomedical
information applications and as a powerful resource for biomedical
information specialists. Copyright by and reprinted with permission of the
Medical Library Association.</P>
<P>Tuttle M, Sherertz D, Olson N, Erlbaum M, Sperzel D, Fuller L, Nelson
S. Using Meta-1-the 1st version of the UMLS Metathesaurus. Proc Annu Symp
Comput Appl Med Care 1990:131-5. The National Library of Medicine (NLM) is
developing the Unified Medical Language System (UMLS) to provide uniform
access to the world's biomedical knowledge. The foundation of the UMLS is
a metathesaurus of concept names, or terms. Meta-1, the first version of
the Metathesaurus, was synthesized from existing biomedical nomenclatures
and classification systems, and it contains in excess of 100000 terms,
including all those from MeSH and DSM, and a portion of those from SNOMED,
ICD, CPT, LCSH, COSTAR and other sources. These names are arranged and
labeled so as to help answer the questions, 'What is it called?' and
'Where can I find out more about it?' The first question is referred to as
the naming problem, and the second as the location problem.' Meta-1 is a
source of lexical diversity and semantic locality with which to address
these problems in biomedicine. While the NLM will be using Meta-1 in the
UMLS, non-NLM developers and users may wish to use Meta-1 to help solve
their own naming and location problems. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Tuttle MS, Nelson SJ, Fuller LF, Sherertz DD, Erlbaum MS, Sperzel WD,
Olson NE, Suarez-Munist ON. The semantic foundations of the UMLS
metathesaurus. Medinfo 1992;7(Pt 2):1506-11. The United States National
Library of Medicine (NLM) has issued two (annual) versions of the Unified
Medical Language System (UMLS) Metathesaurus, with the third scheduled for
Fall, 1992. The UMLS project is a long-term initiative intended to
develop, for use by both care-givers and researchers, a uniform interface
to biomedical knowledge available in electronic form. The project has been
in a component evaluation phase since the release of Meta-1.0, the first
version of the Metathesaurus, and an accompanying Semantic Network, in
October, 1990. The Metathesaurus, so called because it is a synthesis and
enhancement of existing naming and classification systems, is the central
naming component of the UMLS, a place where both users and programs can
retrieve the names of biomedical concepts, and information about how the
names and concepts relate to one another, and how they are used in
selected machine readable sources.</P>
<P>Tuttle MS, Olson NE, Campbell KE, Sherertz DD, Nelson SJ, Cole WG.
Formal properties of the Metathesaurus. Proc Annu Symp Comput Appl Med
Care 1994:145-9. The Metathesaurus is a machine-created, human edited and
enhanced synthesis of authoritative biomedical terminologies. Its formal
properties permit it to be a) exploited by computers, and b) modified and
enhanced without compromising that usage. If further constraints were
imposed on the existence and identity of Metathesaurus relationships,
i.e., if every Metathesaurus concept had a genus and a differentia, then
the Metathesaurus could be converted into an Aristotelian Hierarchy. In
this sense, a genus is a concept that classifies another concept, and a
differentia is a concept that distinguishes the classified concept from
all other concepts in the same class. Since, in principle, these
constraints would make the Metathesaurus easier to leverage and maintain
computationally, it is interesting to ask to what degree the maintenance
and enhancement procedures now in place are producing a Metathesaurus that
is also an Aristotelian Hierarchy. Given a liberal interpretation of the
current Metathesaurus schema, the proportion of the Metathesaurus that is
Aristotelian in each annual version is increasing in spite of dramatic
concurrent increases in the number of Metathesaurus concepts. Without
formality there is no modifiability nor scalability. We need formal
methods and computer-based tools that can help us with the task [of
controlled medical vocabulary construction]. We need research in which
controlled vocabulary development is the focus rather than a stepping
stone for work on other theories and applications. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Yang Y, Chute CG. A schematic analysis of the Unified Medical Language
System. Proc Annu Symp Comput Appl Med Care 1991:204-8. The UMLS is a
complex collection of medical terms and relationships derived from
standard classifications. Appreciating the scope and layout of these
relations from text descriptions of relational schema is difficult. The
graphical technique of Logical Data Structure (LDS) representation was
employed to illustrate the UMLS schema as a data abstraction, affording
additional insights that might otherwise escape notice. An LDS
representation of the Metathesaurus offers the following advantages: 1)
the separation of a viewpoint from physical data structures enables a
global outline of the contents; 2) the graphical map makes the
interrelation of data visible; and 3) the logical entities explicitly
reflect the decision-making which was implicit or ambiguous in the
relational scheme. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P><A
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<HR>
<UL>
<LI>
<UL>
<LI><STRONG><A name=2b>Development and
Maintenance</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Sherertz DD, Olson NE, Tuttle MS, Erlbaum MS. Source inversion and
matching in the UMLS Metathesaurus. Proc Annu Symp Comput Appl Med Care
1990:141-5. One of three knowledge sources being developed as NLM'S UMLS
is a biomedical thesaurus, called the Metathesaurus. It contains
inter-term relationships across six biomedical nomenclatures and
classification systems, derivable from lexical mapping techniques. The
first public version, META-1, was built in two stages: source inversion
and source matching. Versions for the six sources were obtained in
machine-readable form. Source specific techniques were derived empirically
to analyze the information structure and content of each source. The
results of each analysis were used to guide the inversion of the
corresponding source, resulting in a homogeneous representation for all
sources. The core concepts of META-1 come primarily from MEDLINE index
terms (MeSH). Previous work on lexical mapping developed algorithmic
methods to link concepts in different sources. These methods were refined
iteratively, and used to implement a META-1 matching engine. The initial
version of META-1 was constructed with this engine, by matching the META-1
core concepts to the other sources. This version of META-1 was edited and
enhanced by domain experts, after the inclusion of supplementary
information, to produce the first publicly released version of META-1.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Sherertz DD, Olson NE, Tuttle MS, Sperzel WD, Erlbaum MS, Fuller LF.
The META-1 engine: a database methodology used in building the UMLS
METATHESAURUS. Medinfo 1992;7(Pt 1):144-9. Three knowledge sources are
being developed as part of the US NLM's UMLS project. The largest of these
is a biomedical thesaurus, called the METATHESAURUS. META-1 and META-1.1
(or META-1*), the first two versions of the METATHESAURUS, contain term
attributes and relationships across a number of biomedical nomenclatures
and classification systems. Entries in META-1* result from human experts
editing entries computed by an explicit database methodology. A database
engine is implemented to manage the steps used to build up the entries of
META-1* before editing, and to control the application of facts generated
by editing the computed META-1* entries. This engine maintains and
manipulates a database of facts about the entries in META-1*, and, prior
to editing produces a METATHESAURUS that is probably correct, in the sense
that all of the inter-term relationships are derivable solely from data
within the sources. The methodology used by this engine controls the
management of complexity in the METATHESAURUS, as facts change and evolve,
allowing many iterations of META-1* to be computed and analyzed.</P>
<P>Sherertz DD, Tuttle MS, Blois MS, Erlbaum MS. Intervocabulary mapping
within the UMLS: the role of lexical matching. Proc Annu Symp Comput Appl
Med Care 1988:201-6. Within the NLM's UMLS Project, one challenge is
mapping concepts from one information resource to another. While a
complete solution to this problem requires construction of a comprehensive
biomedical thesaurus, the present research provides evidence that
considerable progress can be made with a straightforward lexical approach.
Furthermore, such a lexical approach is the only practical way to begin
construction of, and maintain, any such thesaurus. Related research has
demonstrated the regularity of word usage within the context of
biomedicine. This regularity suggests that mapping between biomedical
information resources that have a constrained vocabulary can use lexical
matching techniques with considerable success. A method has been developed
to map 'phrases' from candidate sources to MeSH. In one experiment, this
method attempts to map 834 disease names from the disease descriptions
composed at UCSF for the UMLS. In a second experiment, the same method
attempts to map disease attributes from these diseases. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Sherertz DD, Tuttle MS, Olson NE, Erlbaum MS, Nelson SJ. Lexical
mapping in the UMLS metathesaurus. Proc Annu Symp Comput Appl Med Care
1989:494-9. A critical knowledge source being developed as part of the
NLM's UMLS (National Library of Medicine's Unified Medical Language
System) project is a biomedical thesaurus, called the metathesaurus.
Central to the metathesaurus will be interterm relationships, across
several biomedical nomenclatures and classification systems, which are
derivable from lexical mapping techniques. Previous UMLS research on
intervocabulary mapping elaborated these techniques. During the Fall of
1988, they were extended and used to build Meta-0, a 2000-concept
demonstration metathesaurus. Meta-0 was composed primarily of the most
frequently occurring MEDLINE index terms from MeSH (Medical Subject
Headings), and MeSH will be the main source of concepts for Meta-1, the
initial public version of the metathesaurus. Review of Meta-0 suggested
several refinements to the methodology for building Meta-1. These include
labeling MeSH entry terms as lexical variants or synonyms before linking
them to other sources. Later work refined algorithmic methods that detect
lexical variants in MeSH. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Sperzel D, Erlbaum M, Fuller L, Sherertz D, Olson N, Schuyler P, Hole
W, Savage A, Passarelli P, Tuttle M. Editing the UMLS Metathesaurus:
review and enhancement of a computer knowledge source. Proc Annu Symp
Comput Appl Med Care (1990):136-40. The paper describes the editing of
Meta-1, the first official version of the National Library of Medicine's
(NLM) Unified Medical Language System (UMLS) Metathesaurus. After a
preliminary version of Meta-1 was generated by automated techniques, it
was edited by domain experts. The goal of editing was to enhance
approximately 30000 Metathesaurus entries and to correct 'errors of
commission' introduced by the automated techniques. Enhancements were made
by assigning semantic types (such as 'Disease or Syndrome' or 'Virus') and
lexical tags (such as 'eponym') to the Meta-1 entries. The production of
Meta-1 required balancing the costs of human and computational resources
appropriately, and it may illustrate a paradigm for the construction of
large biomedical information resources. The tool-supported process of
editing Meta-1, as well as some of the issues that arose during this
endeavor, are presented. Despite its large scale, the Meta-1 editing task
was accomplished within the specified constraints. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Sperzel WD, Tuttle MS. Updating the UMLS metathesaurus: A model. Proc
Annu Symp Comput Appl Med Care 1989:488-93. The Unified Medical Language
System (UMLS) is intended to support uniform access of machine-readable
biomedical information resources. The foundation of the UMLS is a
metathesaurus, which will link terms in different biomedical
nomenclatures. Because the resources and nomenclatures continue to evolve,
the metathesaurus must evolve with them. Thus, an important criterion for
the design of the metathesaurus is the accommodation of change. A model of
such accommodation is presented. A key design decision was the
representation of the metathesaurus, and prospective updates, as a
database of "facts." Particular emphasis is placed on database operations
that use the results of internomenclature lexical matching to collapse
entries from different nomenclatures into metathesaurus entries. The
implementation of this model for a simplified version of the metathesaurus
is described. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Sperzel WD, Tuttle MS, Olson NE, Erlbaum MS, Saurez-Munist O, Sherertz
DD, Fuller LF. The Meta-1.2 engine: a refined strategy for linking
biomedical vocabularies. Proc Annu Symp Comput Appl Med Care 1992:304-8.
This paper presents a preliminary description of the database schema and
associated procedures that are the foundation for the engine that will
produce Meta-1.2. Meta-1.2 is the next incarnation of the Metathesaurus,
which is one of the principal components of the National Library of
Medicine's Unified Medical Language System (UMLS). We use the word engine
as a generic term that includes a database and the programs that operate
on it. While this design builds heavily upon previous work, it
incorporates some major changes in philosophy. A major hypothesis is that
the simple representation described here is suitable for any controlled
vocabulary in the biomedical domain. Indeed, this hypothesis is central to
a strategy for producing future versions of the Metathesaurus and for
supporting collaboration with people who wish to contribute additional
terms and relationships to the Metathesaurus. Another change involves the
representation of classes and relationships. The revised database schema
includes an explicit representation of the source or authority for
relationships, which is analogous to the way that the sources of terms
have been represented since the first version of the Metathesaurus. A
sequence of steps utilizing the new representations to produce the
Metathesaurus is presented. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Suarez-Munist ON, Tuttle MS, Olson NE, Erlbaum MS, Sherertz DD, Lipow
SS, Cole WG, Keck KD, Davis AN, Hole WT, et al. MEME II supports the
cooperative management of terminology. Proc AMIA Fall Symp 1996:84-8.
Health care enterprises need enterprise-wide terminologies to compare,
reuse and repurpose health care descriptions. But once they are created,
these terminologies need to be maintained and enhanced to sustain their
utility and that of the descriptions encoded with them. MEME II
(Metathesaurus Enhancement and Maintenance Environment, Version II)
supports the required activities and enables enterprises to leverage their
investment in terminology and descriptions by permitting remote --
extra-enterprise -- enhancements to terminology to be incorporated
locally, and local -- intra-enterprise -- enhancements to be shared
remotely. MEME II represents all changes to terminologies as data, or
"actions" that can be interpreted by an "action engine." These actions, or
messages, represent semantic "units of work" that can be interpreted by
other copies of MEME II. The exchange of update messages increases the
likelihood that "the comparability of terminology-based health care
descriptions can be sustained. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Tuttle MS, Blois MS, Erlbaum MS, Sherertz DD, Nelson SJ. Toward a
bio-medical thesaurus: Building the foundation of the UMLS. Proc Annu Symp
Comput Appl Med Care 1988:191-5. The Unified Medical Language System
(UMLS) is being designed to provide a uniform user interface to
heterogeneous machine-readable biomedical information resources, such as
bibliographic databases, genetic databases, expert systems and patient
records. Such an interface will have to recognize different ways of saying
the same thing and provide links to related ways of saying things. One way
to represent the necessary associations is by using a domain thesaurus. As
no such thesaurus exists, and because, once built, it will be both sizable
and in need of continuous maintenance, its design should include a
methodology for building and maintaining it. A methodology utilizing
lexically expanded schema inversion and a design, called T. Lex, is
proposed, which forms an approach to the problem of defining and building
a biomedical thesaurus. It is argued that the semantic locality implicit
in such a thesaurus will support model-based reasoning in biomedicine.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Tuttle MS, Sherertz DD, Erlbaum MS, Olson NE, Nelson SJ. Implementing
meta-1: The first version of the UMLS metathesaurus. Proc Annu Symp Comput
Appl Med Care 1989:493-7. The Unified Medical Language System (UMLS) is
being designed to provide uniform access to computer-based resources in
biomedicine. For the foreseeable future, the foundation of the UMLS will
be a metathesaurus of concepts, synthesized from existing sources,
including MeSH, SNOMED, ICD-9-CM, CPT-4, DSM-III, and other biomedical
nomenclatures and classification systems. In Meta-1, the first version of
the metathesaurus, the synthesis is being implemented using a three-part
methodology: concept names (terms) and intrasource relationships, such as
synonymy, have been extracted from each source and converted to a
homogeneous representation, intersource lexical matches have been used to
combine terms from different sources into metathesaurus entries; and some
30000 of these entries, those containing MeSH terms and a selected sample
of terms from other domains, will be reviewed by humans, enhanced, and
modified, as appropriate. This methodology must eventually support
incremental development and an audit trail, and it must preserve
relationships added during human review. The 30,000 Meta-1 entries will
contain in excess of 60,000 biomedical terms, and these terms will
participate in more than 100,000 thesaurus relationships. These
"normative" relationships will be supplemented by "empirical"
relationships computed from certain UMLS resources. The first of the
empirical relationships will be counts of the occurrence and co-occurrence
of Meta-1 concepts in MEDLINE. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Tuttle MS, Sherertz DD, Erlbaum MS, Sperzel WD, Fuller LF, Olson NE,
Nelson SJ, Cimino JJ, Chute CG. Adding your terms and relationships to the
UMLS Metathesaurus. Proc Annu Symp Comput Appl Med Care 1991:219-23. The
National Library of Medicine's Unified Medical Language System
Metathesaurus contains the richest single corpus of biomedical names in
existence. Yet, developers wishing to make use of the Metathesaurus will
be confronted by users who want to add local terminology and relationships
not already represented there. We urge developers to fill those needs,
while, at the same time, they plan for the many consequences of unilateral
Metathesaurus enhancement. Foremost among these consequences is the need
to maintain local enhancements across subsequent releases of the
Metathesaurus. These problems are illustrated via examples of candidate
Metathesaurus enhancement terms in use at the Columbia-Presbyterian
Medical Center (CPMC), at the Mayo Clinic, and in Current Disease
Descriptions (CDD). Sharing and reuse of Metathesaurus enhancement methods
may permit local enhancements to be used at other sites, and it may permit
the global Metathesaurus utilization effort to benefit from economies of
scale. Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Tuttle MS, Suarez-Munist ON, Olson NE, Sherertz DD, Sperzel WD, Erlbaum
MS, Fuller LF, Hole WT, Nelson SJ, Cole WG, et al. Merging terminologies.
Medinfo 1995;8(Pt 1):162-6. A terminology is a systematic, authoritative
collection of concept names, or terms, in some domain. No single
terminology names all th0e important concepts in biomedicine. One approach
to creating a more comprehensive biomedical terminology is to merge
existing biomedical terminologies, as the UMLS Metathesaurus has done for
the last six years. Because existing terminologies may overlap--for
example, one terminology may name a concept also named by another
terminology--the terminologies in the Metathesaurus must be merged. Some
terminologies suggest merges through their structure or content e.g., they
suggest synonyms or connections to other terminologies; other merges can
be suggested by algorithm. Regardless, all merges in the Metathesaurus
must be approved by a human editor with appropriate domain knowledge. By
the time Meta-'96 is released early in 1996, one prototype and seven
released versions of the Metathesaurus will have been produced by a
sequence of four qualitatively different methods, named for the way in
which they merge terms: #1 Term Rewrite Rules, #2 Transitive Closure on
Facts, #3 Fact-at-a-Time Concept Merging, and #4 Action-at-a-Time Object
Processing. The development of each method has been constrained by the
annual Metathesaurus release schedule. The first two methods made the best
use of limited computational resources, and the last two make better use
of human editing resources.</P><A
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<HR>
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<UL>
<LI><STRONG><A name=2c>Content
Coverage</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Bishop CW, Ewing PD. Transferring knowledge from one system to another.
Proc Annu Symp Comput Appl Med Care 1994:967. Although knowledge is
contained in many systems, moving it from one system to another is not an
easy task because each system is tailored in its own unique way and
because knowledge configurations are usually copyrighted. To populate our
FRAMEMED knowledge base we turned to the NLM Metathesaurus as a
readily-available open source of knowledge. We were disappointed by the
greatly variable granularity of the concepts and the lack of definitions
that could be borrowed. Some reference books in electronic form seem
attractive but reformatting will require excessive human intervention and
copyright negotiation. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Campbell JR, Kallenberg GA, Sherrick RC. The clinical utility of META:
an analysis for hypertension. Proc Annu Symp Comput Appl Med Care
1992:397-401. To evaluate the clinical completeness of the National
Library of Medicine Metathesaurus(META), we coded the conceptual
information found in 2000 problem oriented (SOAP) notes for hypertension
from one COSTAR site. To minimize the effects of practice idiosyncracy, we
analyzed an additional 500 notes from a second, geographically remote
site. Concepts occurring at either site numbered 1337. We classified
concepts occurring at both sites as core concepts and these numbered 121.
We attempted to find a matching concept of the proper semantic type in
META for each of the items. All matching was done by program with a manual
review by a physician. The overall success rate for matching was: [table:
see text]. We observed the greatest frequency of unmatched concepts in
physical examination, medications, symptoms, personal behavior,
non-medical therapies and counselling. We conclude that the current
release of META is not sufficiently rich to describe the process of care
in the ambulatory management of hypertension. However, the construction
and breadth of the current scheme holds promise for medical knowledge
representation and translation. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Campbell JR, Payne TH. A comparison of four schemes for codification of
problem lists. Proc Annu Symp Comput Appl Med Care 1994:201-5. We set out
to evaluate the completeness of four major coding schemes in
representation of the patient problem list: the Unified Medical Language
System (UMLS, 4th edition), the Systematized Nomenclature of Medicine
(SNOMED International), the Read coding system (version 2), and the
International Classification of Diseases (9th Clinical
Modification)(ICD-9-CM). We gathered 400 problems from patient records at
primary care sites in Omaha and Seattle. Matching these against the best
description found in each of the coding schemes, we asked five medical
faculty reviewers to rate the matches on a five-point Likert scale
assessing their satisfaction with the results. For the four schemes, we
computed the following rates of dissatisfaction, satisfaction, and average
scores: [table: see text]. From this analysis, we conclude that UMLS and
SNOMED performed substantially better in capturing the clinical content of
the problem lists than READ or ICD-9-CM. No scheme could be considered
comprehensive. Depending on the goal of systems developers, UMLS and
SNOMED may offer different, and complementary, advantages. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Chute CG, Cohn SP, Campbell KE, Oliver DE, Campbell JR. The content
coverage of clinical classifications. For The Computer-Based Patient
Record Institute's Work Group on Codes &amp; Structures. J Am Med Inform
Assoc 1996 May-Jun;3(3):224-33. BACKGROUND AND OBJECTIVE: Patient
conditions and events are the core of patient record content.
Computer-based records will require standard vocabularies to represent
these data consistently, thereby facilitating clinical decision support,
research, and efficient care delivery. To address whether existing major
coding systems can serve this function, the authors evaluated major
clinical classifications for their content coverage. METHODS: Clinical
text from four medical centers was sampled from inpatient and outpatient
settings. The resultant corpus of 14,247 words was parsed into 3,061
distinct concepts. These concepts were grouped into Diagnoses, Modifiers,
Findings, Treatments and Procedures, and Other. Each concept was coded
into ICD-9-CM, ICD-10, CPT, SNOMED III, Read V2, UMLS 1.3, and NANDA; a
secondary reviewer ensured consistency. While coding, the information was
scored: 0 = no match, 1 = fair match, 2 = complete match. RESULTS:
ICD-9-CM had an overall mean score of 0.77 out of 2; its highest subscore
was 1.61 for Diagnoses. ICD-10 scored 1.60 for Diagnoses, and 0.62
overall. The overall score of ICD-9-CM augmented by CPT was not materially
improved at 0.82. The SNOMED International system demonstrated the highest
score in every category, including Diagnoses (1.90), and had an overall
score of 1.74. CONCLUSION: No classification captured all concepts,
although SNOMED did notably the most complete job. The systems in major
use in the United States, ICD-9-CM and CPT, fail to capture substantial
clinical content. ICD-10 does not perform better than ICD-9-CM. The major
clinical classifications in use today incompletely cover the clinical
content of patient records; thus analytic conclusions that depend on these
systems may be suspect. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Chute CG, YangY, Tuttle MS, Sherertz DD, Olson NE, Erlbaum MS. A
preliminary evaluation of the UMLS Metathesaurus for patient record
classification. Proc Annu Symp Comput Appl Med Care 1990:161-5. The UMLS
project seeks to provide a unified interface to biomedical knowledge
resources. Patient medical records are an enormous repository of clinical
intervention and outcome, and are drawing increasing attention in the
pursuit of quality assurance, outcomes research, and epidemiologic
analysis. The authors sought to evaluate an unedited version of the
preliminary UMLS Metathesaurus, Meta-1, for the automated coding of
medical diagnosis and surgical procedures. Identical evaluations were
undertaken using SNOMED and the Mayo Clinic indexing lexicon. Meta-1
performed comparably to the comparison clinical indexing system, although
all systems exhibited problems associated with clinical attribute levels
and modifier combinations. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Cimino JJ. Representation of clinical laboratory terminology in the
Unified Medical Language System. Proc Annu Symp Comput Appl Med Care
1991:199-203. The Unified Medical Language System (UMLS) was examined to
determine its coverage of clinical laboratory terminology in use at the
Columbia-Presbyterian Medical Center (CPMC). The Metathesaurus (Meta-1)
contains exact matches for 30% of 1460 CPMC laboratory terms and near
matches for an additional 42%, with better coverage of atomic-level
concepts (substance terms) than complex ones (tests and panels). The
Semantic Network includes types for representing laboratory procedures
(2), measured substances (at least 56) and sampled substances (at least
14), but no type to represent specimens. Few of the UMLS semantic
relationships are applicable to the CPMC vocabulary. These results have
implications for the utility of the UMLS for linking clinical databases to
electronic medical information sources. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Evans DA. The language of medicine and the modeling of information. In:
Evans DA, Patel VL , editors. Advanced models of cognition for medical
training and practice; Berlin: Springer-Verlag; 1992. p. 43-67.</P>
<P>Friedman C. The UMLS coverage of clinical radiology. Proc Annu Symp
Comput Appl Med Care 1992:309-13. The informational content of clinical
radiology reports was examined to determine the coverage of the Unified
Medical Language System (UMLS) in relation to the terminology used by
physicians in the Radiology Department of Columbia Presbyterian Medical
Center (CPMC). The UMLS semantic network contained 17 semantic types which
were compatible with the types of clinical information in the reports. The
type of semantic categories missing from the UMLS consisted mainly of
modifier information relating to certainty, degree, and change type of
information. This type of information formed a substantial part of the
domain. Although most of the informational categories were found in the
UMLS semantic network, most of the domain terms were not. Our results
strongly suggest that the UMLS could be a significant tool for developing
clinical text processing applications if it were extended to cover
clinical domains. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Fuller L, Hole W, Olson N, Schuyler P, Tuttle M. Drug and chemical
entries in Meta-1. Proc Annu Symp Comput Appl Med Care 1990:146-50.
Thirty-two percent of the concepts in the National Library of Medicine's
UMLS Metathesaurus, Meta-1, are the names of biomedically important
chemicals. The paper describes the origin of the chemical terms included
in Meta-1, the structure and information content of these records, and the
potential uses of these concepts to access chemical information in
biomedical databases. Data is also presented quantitatively describing the
subjects of the articles in the biomedical literature and the frequency
with which articles include chemical subjects. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Huff SM, Warner HR. A comparison of Meta-1 and HELP terms: implications
for clinical data. Proc Annu Symp Comput Appl Med Care 1990:166-9. Terms
from the HELP System's vocabulary were matched with Meta-1 terms on a word
by word basis as well as on a phrase by phrase basis with the goal of
exploring what steps might need to be taken if some future version
(Meta-N) of the UMLS Metathesaurus were to be used to represent clinical
data. Word by word matching revealed that 54% of HELP words were present
in Meta-1, while 8% of HELP phrases had a corresponding phrase. The words
that did not match in HELP were mostly adjectives and adverbs after taking
into account misspellings and abbreviations. Phrase matches were low
because of the inclusion of adjectives and adverbs in HELP clinical terms.
If some future version of the Metathesaurus is to be used for
representation of clinical data additional terms are needed as well as a
grammar that permits construction of clinical phrases that include
modifiers and time references. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Lange LL. Representation of everyday clinical nursing language in UMLS
and SNOMED. Proc AMIA Fall Symp 1996:140-4. Everyday clinical nursing
language is informal and idiosyncratic. Whether the everyday language of
nurses can be represented by standardized vocabulary systems, such as the
UMLS and SNOMED, was the focus of the study. Computer systems that allow
clinicians to pick terms that are familiar are likely to be better
accepted and thus more effective than systems that impose formal
terminologies on users. Nursing phrases were extracted from handwritten
shift notes, reduced to atomic-level terms, and matched to UMLS and
SNOMED. Exact matches were obtained for 56% of terms in UMLS and 49% in
SNOMED. Fifty-nine semantic types and 24 different source vocabularies
were represented by the terms. Nursing vocabularies were represented by
only 5% of source vocabulary citations. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Lindberg CH. A comparison of the language of patient charts at
Presbyterian University Hospital, Pittsburgh, PA., and the Unified Medical
Language System of the National Library of Medicine (online medical
records) [dissertation]. Pittsburgh (PA): University of Pittsburgh; 1994.
176 p. Available from: University Microforms, Ann Arbor, MI; 9426718. This
dissertation matches the language of online medical records at the
Presbyterian University Hospital in Pittsburgh with the language of the
Unified Medical Language System (UMLS), an experimental thesaurus of
biomedicine developed by the National Library of Medicine. In the future,
the UMLS may serve as an interface between medical charts and the
information in databases such as Medline. The main research question is
whether the UMLS captures the concepts found in medical charts and can
thus be used to bridge the gap between chart terminology and MeSH, the
vocabulary used to access Medline. A sample of 50 records from two
diagnoses was compared to the UMLS. A statistical formula selected
potentially useful non-matches, which were then analyzed to determine
whether the missing concepts are wholly or partially present in another
form in MeSH. Seventy percent of the missing terms are either broader
terms than MeSH headings or synonyms of chart terms/concepts.
Approximately 19% of the dropped terms could not form a strong map to
MeSH. The study indicates that, since so many chart terms are found in
some form, a chart-generated search can link to many related concepts in
MeSH, but a significant number of chart concepts must be added to the UMLS
or cross referenced to MeSH. Provided by UMI. </P>
<P>Moving toward international standards in primary care informatics:
clinical vocabulary. Conference Summary Report. 1995 Nov 1-2; New Orleans.
Rockville (MD): Agency for Health Care Policy and Research; 1996 Oct. 35
p. (AHCPR pub. no. 96-0069) Available also from <A
"http://www.ahcpr.gov/research/pcinform/">http://www.ahcpr.gov/research/pcinform/</A>.</P>
<P>Mullins HC, Scanland PM, Collins D, Treece L, Petruzzi P Jr., Goodson
A, Dickinson M. The efficacy of SNOMED, Read codes, and UMLS in coding
ambulatory family practice clinical records. Proc AMIA Fall Symp
1996:135-9. This study was initially developed as a traditional
quantitative study to determine the level of match of identified clinical
terms in three (3) clinical vocabularies. To address concerns raised by a
review of the literature and our own experience, a supplemental study to
collect qualitative data was added. Dictated progress notes from a
stratified sample of patient visits over a period of four (4) years were
used to obtain a representative sample of terms. A total of 144 progress
notes were selected taking into consideration the usual demographics plus
additional variables. From the 144 clinical notes, 864 terms were
extracted and evaluated by level of match. The within-term effect was
highly significant (F=58.69, p&lt;-.001), indicating significant
differences in the mean level of match for the three coding systems.
Qualitative findings suggest that this and other published studies may not
answer questions about the "efficacy of available clinical vocabularies in
coding ambulatory family practice clinical records", and additional
studies are needed which must be carefully structured and utilize a
standardized procedure. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>O'Keefe KM, Sievert M, Mitchell JA. Mendelian inheritance in man:
diagnoses in the UMLS. Proc Annu Symp Comput Appl Med Care 1993:735-9.
Because they deal with many distinct but rare inheritance diseases,
geneticists have difficulty translating from their codes to other
biomedical coding schemes. The objective of this research was to
investigate the potential uses and difficulties of using the UMLS
Metathesaurus for genetic diagnoses and to make recommendations to UMLS
developers for improvements in UMLS for common genetic disorders. The 110
most common Mendelian Inheritance in Man disorders from the Missouri
Genetic Disease Program over the period of one year were translated into
MeSH, ICD and SNOMED. The more common diseases are more likely to be
mapped than the rarer ones. Diseases with a proven genetic inheritance
pattern are more likely to be mapped than those with speculated
inheritance patterns. Approximately one third of all diagnoses were not
mapped across all three coding schemes in Meta-1.2. The ICD coding scheme
was found to be too broad to be meaningful for genetic diagnosis or
epidemiological purposes. MeSH and SNOMED need to be made more specific
and complete, and all of the new version of SNOMED needs to be included in
the Metathesaurus. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Payne TH, Martin DR. How useful is the UMLS metathesaurus in developing
a controlled vocabulary for an automated problem list? Proc Annu Symp
Comput Appl Med Care 1993:705-9. We are developing a set of problem list
phrases to be used in the automated problem list of a prototype clinical
computing system. Because of the large number of terms in the Unified
Medical Language System (UMLS) and the links between them, we are
experimenting with the use of the UMLS as the foundation for our problem
list phrase set. We have found the UMLS to be very useful for this
project, but that it lacks many phrases clinicians wish to include in the
problem list. Internal linkages between phrases provided in the UMLS are
not well suited to our needs. We plan to continue our use of the UMLS but
to add problem list phrases and linkages between phrases to support
browsing and decision support applications. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Rosenberg KM, Coultas DB. Acceptability of Unified Medical Language
System terms as substitute for natural language general medicine clinic
diagnoses. Proc Annu Symp Comput Appl Med Care 1994:193-7. The
acceptability of using the Unified Medical Language System (UMLS) concept
phrases to substitute for physicians' diagnosis statements was
investigated. Physician diagnosis statements recorded in the University of
New Mexico's General Medicine Clinic were input into a computer program
that automatically finds the best matching UMLS concept phrases. The
computer program written in C++ integrates UMLS searching and browsing
with a graphical user interface. Five attending physicians in the
Department of Internal Medicine rated the acceptability of the UMLS
concept phrase as a substitute for the original physician statement. One
hundred and ninety-five patients' notes were examined with 447 diagnosis
statements recorded of which 271 statements were unique. Attending
physicians rated their satisfaction with the automated UMLS substitutes on
a scale of 1 (extremely dissatisfied) to 5 (extremely satisfied).
Intrarater (mean 0.94) and interrater correlations (mean 0.75) were high.
The mean rating was 4.0 (quite satisfied). Most (73%) of the substitution
were satisfactory (rating of 4 or 5), 16% were neutral (rating of 3), and
21% were unsatisfactory (rating of 1 or 2). A review of the substitutions
showed a frequent lack of clinical modifier terms in UMLS as has been
previously described. Comparison to a previous study shows the broader
term coverage of UMLS to be a more acceptable source of diagnosis codes
than using International Classification of Diseases revision 9 alone.
These results suggest that UMLS can be an effective tool for coding
unconstrained physician diagnoses. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Sato L, McClure RC, Rouse RL, Schatz CA, Greenes RA. Enhancing the
Metathesaurus with clinically relevant concepts: anatomic representations.
Proc Annu Symp Comput Appl Med Care 1992:388-91. To create a comprehensive
taxonomy for medical concepts it is necessary to identify gaps and
reconcile differences that exist between clinical, bibliographic, and
other source vocabularies. As part of the Unified Medical Language System
project, we have proposed enhancements to the Metathesaurus by the
inclusion of terms from two source vocabularies with different unique
perspectives or views. This process has disclosed a number of issues that
arise as complexity increases. These issues must be resolved if the
resultant Metathesaurus is to support the variety of uses for which it is
intended. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Warren JJ, Campbell JR, Palandri MK, Stoupa RA. Analysis of three
coding schemes: can they capture nursing care plan concepts? Proc Annu
Symp Comput Appl Med Care 1994:962.</P>
<P>Zielstorff RD, Cimino C, Barnett GO, Hassan L, Blewett DR.
Representation of nursing terminology in the UMLS Metathesaurus: a pilot
study. Proc Annu Symp Comput Appl Med Care 1992:392-6. To see whether the
National Library of Medicine's Metathesaurus (tm) includes terminology
relevant to clinical nursing practice, two widely used nursing
vocabularies were matched against the Meta. The two nursing vocabularies
are 1) the North American Nursing Diagnosis List of Approved Diagnoses;
and 2) the Omaha System, a vocabulary of problems and interventions
developed by the Omaha Visiting Nurses Association. First, the terms were
scanned against Meta in their native form, with phrases and combinations
intact. This produced a relatively low percentage of exact matches (12%).
Next, the terms were separated into core concepts and modifiers and the
analysis was repeated. The percentage of exact matches to terms in Meta
increased to 32%. However, the semantic types of the split terms often
were not equivalent to the semantic types of the phrases from which the
split terms were derived; also, in some cases, terms returned as exact
matches had different meanings in Meta. Automatic scanning for lexical
matches is a helpful first step in searching for vocabulary representation
in Meta, but term-by-term search for context, semantic type and definition
is essential. However, it seems clear that representation of nursing
terminology in the Metathesaurus needs to be expanded. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=2d>Information Sources Map</A></STRONG><BR></LI></UL>
<HR>
<P>Masys DR. An evaluation of the source selection elements of the
prototype UMLS Information Sources Map. Proc Annu Symp Comput Appl Med
Care 1992:295-8. The Information Sources Map (ISM) is a component of the
National Library of Medicine's Unified Medical Language System (UMLS)
project. The ISM is intended to provide both human-readable and
machine-interpretable information about the content, scope, and access
conditions for various information sources such as databases, expert
systems, and the organizations which make these information sources
available. Automated source selection is supported by three types of
indexing in the ISM: Medical Subject Heading (MeSH) terms and subheadings;
Semantic Types from the UMLS Semantic Network; and Semantic Type
Relations, which depict pairs of semantic types joined by a relationship
chosen from the Semantic Network. This paper reports a study of the recall
and precision of the source selection elements in the prototype version of
the ISM. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Masys DR, Humphreys BL. Structure and function of the UMLS information
sources map. Medinfo 1992;7(Pt 2):1518-21. A health professional seeking
information which is represented in computerized format faces formidable
difficulties in determining which information sources may be relevant to a
particular question, and in gaining access to that information. The first
version of a new UMLS data file called the Information sources map (ISM)
has been created to address this problem. The ISM is intended to provide
both human-readable and machine-interpretable information about the
content, scope, and access conditions for various information sources such
as databases, expert systems, and the organizations which make these
information sources available. The first prototype of the ISM features
indexing elements which support automated source selection; subsequent
versions will encode the logic necessary to connect to and retrieve
information from the sources represented in the ISM file.</P>
<P>Miller PL, Clyman JI, Frawley SJ, Paton JA, Powsner SM, Roderer N,
Shifman MA. NetMenu and a prototype UMLS information sources map. Proc
Annu Symp Comput Appl Med Care 1993:957. This paper describes NetMenu and
an Information Sources Map (ISM), two tools under development to help the
biomedical user find out about a range of network-based information
sources, and to connect automatically to a chosen source. The prototype
ISM is developed as part of the Unified Medical Language System (UMLS)
project of the National Library of Medicine. Both NetMenu and the ISM are
operational at Yale University School Medicine and are available for use
elsewhere. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Miller PL, Frawley SJ, Wright L, Roderer NK, Powsner SM. Lessons
learned from a pilot implementation of the UMLS information sources map. J
Am Med Inform Assoc 1995 Mar-Apr;2(2):102-15. OBJECTIVE: To explore the
software design issues involved in implementing an operational information
sources map (ISM) knowledge base (KB) and system of navigational tools
that can help medical users access network-based information sources
relevant to a biomedical question. DESIGN: A pilot biomedical ISM KB and
associated client-server software (ISM/Explorer) have been developed to
help students, clinicians, researchers, and staff access network-based
information sources, as part of the National Library of Medicine's (NLM)
multi-institutional Unified Medical Language System (UMLS) project. The
system allows the user to specify and constrain a search for a biomedical
question of interest. The system then returns a list of sources matching
the search. At this point the user may request 1) further information
about a source, 2) that the list of sources be regrouped by different
criteria to allow the user to get a better overall appreciation of the set
of retrieved sources as a whole, or 3) automatic connection to a source.
RESULTS: The pilot system operates in client-server mode and currently
contains coded information for 121 sources. It is in routine use from
approximately 40 workstations at the Yale School of Medicine. The lessons
that have been learned are that: 1) it is important to make access to
different versions of a source as seamless as possible, 2) achieving
seamless, cross-platform access to heterogeneous sources is difficult, 3)
significant differences exist between coding the subject content of an
electronic information resource versus that of an article or a book, 4)
customizing the ISM to multiple institutions entails significant
complexities, and 5) there are many design trade-offs between specifying
searches and viewing sets of retrieved sources that must be taken into
consideration. CONCLUSION: An ISMKB and navigational tools have been
constructed. In the process, much has been learned about the complexities
of development and evaluation in this new environment, which are different
from those for Gopher, wide area information servers (WAIS),
World-Wide-Web (WWW), and MOSAIC resources. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Miller PL, Paton JA, Clyman JI, Powsner SM. Prototyping an
institutional IAIMS/UMLS information environment for an academic medical
center. Bull Med Libr Assoc 1992 Jul;80(3):281-7. The paper describes a
prototype information environment designed to link network-based
information resources in an integrated fashion and thus enhance the
information capabilities of an academic medical center. The prototype was
implemented on a single Macintosh computer to permit exploration of the
overall information architecture and to demonstrate the various desired
capabilities prior to full-scale network-based implementation. At the
heart of the prototype are two components: a diverse set of information
resources available over an institutional computer network and an
information sources map designed to assist users in finding and accessing
information resources relevant to their needs. The paper describes these
and other components of the prototype and presents a scenario illustrating
its use. The prototype illustrates the link between the goals of two
National Library of Medicine initiatives, the Integrated Academic
Information Management System (IAIMS) and the Unified Medical Language
System (UMLS). Copyright by and reprinted with permission of the Medical
Library Association.</P>
<P>Miller PL, Wright LW, Frawley SJ, Clyman JI, Powsner SM. Selecting
relevant information resources in a network-based environment: the UMLS
information sources map. Medinfo 1992;7(Pt 2):1512-7. The paper describes
experience in building a prototype information sources map (ISM) as part
of the Unified Medical language System (UMLS) project of the National
Library of Medicine. A test set of 112 representative medically-related
information sources was compiled. The purpose was to explore what type of
coded information should be included in the ISM to help select sources
relevant to a user query. For each ISM entry (describing a particular
information source), two general types of coded information were included.
(1) Coding using MeSH terms and Meta-1 semantic types was used to
characterize the source's subject content. (2) Additional coded
information related to the source's use. The paper discusses experience in
coding the information sources to create the prototype ISM, and describes
a study to assess the utility of the different coded information in
selecting sources relevant to a user query.</P>
<P>Shifman MA, Clyman JI, Paton JA, Powsner SM, Roderer NK, Miller PL.
NetMenu. Experience in the implementation of an institutional menu of
information sources. Proc Annu Symp Comput Appl Med Care 1993:554-8.
NetMenu is a program developed at Yale University, which enables a
straightforward access to online information systems. NetMenu has been
deployed in several diverse settings within the medical center. In the
hospital, NetMenu functions as a front-end for the clinical workstation,
providing access to the hospital information system, the clinical
laboratory computer, a drug database and several bibliographic databases.
The medical libraries utilize NetMenu for both medical education
workstations and for scholarly information workstations. This paper
describes the initial experience in the implementation, support, and
maintenance of NetMenu as an institutional menu of information sources.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Silverstein SM, Miller PL, Cullen MR. An information sources map for
Occupational and Environmental Medicine: guidance to network-based
information through domain-specific indexing. Proc Annu Symp Comput Appl
Med Care 1993:616-20. This paper describes a prototype information sources
map (ISM), an on-line information source finder, for Occupational and
Environmental Medicine (OEM). The OEM ISM was built as part of the Unified
Medical Language System (UMLS) project of the National Library of
Medicine. It allows a user to identify sources of on-line information
appropriate to a specific OEM question, and connect to the sources. In the
OEM ISM we explore a domain-specific method of indexing information source
contents, and also a domain-specific user interface. The indexing
represents a domain expert's opinion of the specificity of an information
source in helping to answer specific types of domain questions. For each
information source, an index field represents whether a source might
provide useful information in an occupational, industrial, or
environmental category. Additional fields represent the degree of
specificity of a source in individual question types in each category. The
paper discusses the development, design, and implementation of the
prototype OEM ISM. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=2e>Distribution Formats and Associated
Tools</A></STRONG><BR></LI></UL>
<HR>
<P>McCray AT, Divita G. ASN.1: defining a grammar for the UMLS knowledge
sources. Proc Annu Symp Comput Appl Med Care 1995:868-72. The Unified
Medical Language System (UMLS) project provides resources on an
experimental basis to the research community. In 1995 the four UMLS
Knowledge Sources have been provided in an additional data format,
Abstract Syntax Notation One (ASN.1). The benefits of ASN.1 are that it
provides a standard, formal grammar for complex data and allows exchange
of that data in a way which is independent of the particular software and
hardware environment in which the data are created and stored. The paper
begins with an introduction to the ASN.1 standard itself. It continues
with a discussion of the ASN.1 implementation of the UMLS Knowledge
Sources and some of the consequences for the newly released UMLS Knowledge
Source Server. It concludes with a discussion of some of the benefits of
using ASN.1 encoded data. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>McCray AT, Razi A. The UMLS Knowledge Source server. Medinfo 1995;8(Pt
1):144-7. The UMLS Knowledge Source server is an evolving tool for
accessing information stored in the UMLS Knowledge Sources. The system
architecture is based on the client-server paradigm wherein remote site
users send their requests to a centrally managed server at the U.S.
National Library of Medicine. The client programs can run on platforms
supporting the TCP/IP communication protocol. Access to the system is
provided through a command-line interface and through an Application
Programming Interface.</P>
<P>McCray AT, Razi AM, Bangalore AK, Browne AC, Stavri PZ. The UMLS
knowledge source server: a versatile internet-based research tool. Proc
AMIA Fall Symp 1996:164-8. The National Library of Medicine's Unified
Medical Language System (UMLS) project regularly distributes a set of
Knowledge Sources to the research community. In 1995 the UMLS data were
made available for the first time through the Internet-based UMLS
Knowledge Source Server. The server can be accessed through three
different client interfaces. The World Wide Web interface allows users to
browse and explore the data and to see how those data are organized in the
UMLS. The command-line interface is best suited for batch processing, and
the application programming interface allows developers at remote sites to
embed calls in their application programs to the Knowledge Source Server.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>McCray AT, Srinivasan S, Browne AC. Lexical methods for managing
variation in biomedical terminologies. Proc Annu Symp Comput Appl Med Care
1994:235-9. Access to biomedical terminologies is hampered by the high
degree of variability inherent in natural language terms and in the
terminologies themselves. The lexicon, lexical programs, databases, and
indexes included with the 1994 release of the UMLS Knowledge Sources are
designed to help users manage this variability. We describe these
resources and illustrate their flexibility and usefulness in providing
enhanced access to data in the UMLS Metathesaurus. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Nelson SJ, Sherertz DD, Tuttle MS, Erlbaum MS. Using MetaCard: a
Hypercard browser for biomedical knowledge sources. Proc Annu Symp Comput
Appl Med Care 1990:151-4. As part of the Unified Medical Language System
(UMLS) project a large metathesaurus (Meta-1) was built. We have adapted a
Hypercard browser of Meta-1 (MetaCard) to enable a user to continue the
browsing process, extending from the Metathesaurus to a variety of
different knowledge sources. These knowledge sources include Current
Disease Description (CDD), Physicians Data Query (PDQ), and Mendelian
Inheritance in Man (MIM). Metacard can also be linked to Grateful Med, the
NLM program which is used to search MEDLINE. A user can, with minimal
training, use MetaCard to access these four different knowledge sources.
The links (how one goes from one knowledge source to another) have been
built on the basis of disease names. In organizing these links, it was
helpful to use CDD as an additional source of knowledge about how diseases
are named in various sources. Further plans are to expand the use of the
Metathesaurus in building links to knowledge sources. The question with
each method of linking used will be to what extent the method provides a
robust linkage whose utility can be anticipated. While future refinements
or developments of links may give additional functionality, the current
linkages are sufficient to provide a useful browsing tool. We believe that
this is so because much of the knowledge in each of these sources is
organized around diseases. Navigation is easy because of the similarities
of the Hypercard interfaces to each of the knowledge sources: a common set
of conventions (e.g. point and click) helps make it work. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Sherertz D, Tuttle M, Cole W, Erlbaum M, Olson N, Nelson S. A HyperCard
implementation of Meta-1.: The first version of the UMLS Metathesaurus.
Proc Annu Symp Comput Appl Med Care 1989:1017-8. The Unified Medical
Language System (UMLS) is being designed to provide uniform access to
computer-based resources in biomedicine. For the foreseeable future, the
foundation of the UMLS will be a "metathesaurus of concepts," synthesized
from existing biomedical nomenclatures. Meta-1, the first version of the
Metathesaurus, will contain all of MeSH, a selection of terms from primary
care, clinical medicine, and other domains, and all terms from SNOMED,
ICD-9-CM, and CPT-4 which "match" them--about 30,000 terms. In addition,
Meta-1 contains information about the occurrence and co-occurrence of its
terms in selected resources, such as MEDLINE. As Meta-1 will contain about
100MB of terms and relationships, it is unlikely that it will be
"printed." Instead, some UMLS applications will support Metathesaurus
"browsing." One way of browsing Meta-1 will be via the Apple Macintosh
application called HyperCard. A demonstration of a HyperCard interface,
called "Meta-Card" will first acquaint viewers with the contents of the
pre-human-review version of Meta-1, and second, illustrate how an
object-oriented interface can be programmed to support various visual
metaphors, e.g. "click-to-get-more-information," and
"click-to-follow-a-semantic-link," and the notion of a Metathesaurus
esthetic. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Tuttle MS, Sperzel WD, Olson NE, Erlbaum MS, Suarez-Munist O, Sherertz
DD, Nelson SJ, Fuller LF. The homogenization of the Metathesaurus schema
and distribution format. Proc Annu Symp Comput Appl Med Care 1992:299-303.
The third version of the UMLS Metathesaurus, Meta-1.2, to be released in
October 1992, will have a simpler schema and simpler distribution formats
than the first two versions, Meta-1.0 and Meta-1.1 released in October
1990 and 1991, respectively. For one thing, it will have only a single
kind of entry (Concept), rather than three (Concept, Related, and
Synonym). Further, the Relational Format, will consist of four logical
relations, or tables, instead of the nearly three score different tables
used to represent the same kind of information in Meta-1.1. These four
tables will contain, respectively, (1) the names of each concept, (2) the
relationships between concepts, (3) attributes of the concepts, and (4) a
word-based index into the concept names. We argue that the new schema and
formats provide a better conceptual model of the Metathesaurus, and
represent the information contained there more uniformly. Even though
these changes are incremental and evolutionary, both users and software
developers should find the Meta-1.2 significantly easier to understand,
and the information contained in it significantly easier to use. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P><A
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<HR>
<H3>UMLS Applications</H3>
<UL>
<LI><STRONG>Vocabulary Construction and Concept Discovery</STRONG><BR>
<UL>
<LI><STRONG><A name=3a>Vocabulary Design, Construction and
Maintenance</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Campbell KE, Musen MA. Representation of clinical data using SNOMED III
and conceptual graphs. Proc Annu Symp Comput Appl Med Care 1992:354-8.
None of the coding schemes currently contained within the Unified Medical
Language System (UMLS) is sufficiently expressive to represent medical
progress notes adequately. Some coding schemes suffer from domain
incompleteness, others suffer from the inability to represent modifiers
and time references, and some suffer from both problems. The recently
released version of the Systematized Nomenclature of Medicine (SNOMED III)
is a potential solution to the data-representation problem because it is
relatively domain complete, and because it uses a generative coding scheme
that will allow the construction of codes that contain modifiers and time
references. SNOMED III does have an important weakness, however. SNOMED
III lacks a formalized system for using its codes; thus, it fails to
ensure consistency in its use across different institutions. Application
of conceptual-graph formalisms to SNOMED III can ensure such consistency
of use. Conceptual-graph formalisms will also allow mapping of the
resulting SNOMED III codes onto relational data models and onto other
formal systems, such as first-order predicate calculus. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Carenini G, Moore JD. Using the UMLS Semantic Network as a basis for
constructing a terminological knowledge base: a preliminary report. Proc
Annu Symp Comput Appl Med Care 1993:725-9. Sharing and reuse of knowledge
bases is recognized in Artificial Intelligence and Medical Informatics as
beneficial, but difficult. Reusing an existing knowledge base can save
considerable time and effort during the knowledge engineering phase, and
facilitates integration of systems. However, the degree to which knowledge
can be shared among different applications is still mainly an empirical
question. In this paper, we describe the preliminary results of our
attempt to reuse the UMLS Semantic Network as an ontology for the
knowledge base of a patient education system. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Cimino JJ. Controlled medical vocabulary construction: methods from the
Canon Group [editorial]. J Am Med Inform Assoc 1994
May-Jun;1(3):296-7.</P>
<P>Cimino JJ. Formal descriptions and adaptive mechanisms for changes in
controlled medical vocabularies. Methods Inf Med 1996 Sep;35(3):202-10.
Comment in: Methods Inf Med 1996 Sep;35(3):211-7; Methods Inf Med 1996
Sep;35(3):218-9. (Eng). Standard controlled medical vocabularies are
typically based on a coding scheme, while medical informatics applications
tend to have a more formal conceptual foundation. When such applications
attempt to use data coded with standard vocabularies, problems can arise
when the standard vocabulary changes over time. A formal taxonomy is
presented for describing the semantic changes which can occur in a
vocabulary, such as simple addition, refinement, precoordination,
disambiguation, redundancy, obsolescence, discovered redundancy, major
name changes, minor name changes, code reuse, and changed codes. The
taxonomy is described that used to effect change in one concept-based
vocabulary (the Medical Entities Dictionary), and the utility of the
approach is demonstrated by applying it to the changes appearing in the
1994 release of the International Classification of Diseases, Ninth
Edition, with Clinical Modifications (ICD-9-CM). </P>
<P>Cimino JJ, Clayton PD. Coping with changing controlled vocabularies.
Proc Annu Symp Comput Appl Med Care 1994:135-9. For the foreseeable
future, controlled medical vocabularies will be in a constant state of
development, expansion and refinement. Changes in controlled vocabularies
must be reconciled with historical patient information which is coded
using those vocabularies and stored in clinical databases. This paper
explores the kinds of changes that can occur in controlled vocabularies,
including adding terms (simple additions, refinements, redundancy and
disambiguation), deleting terms, changing terms (major and minor name
changes), and other special situations (obsolescence, discovering
redundancy, and precoordination). Examples are drawn from actual changes
appearing in the 1993 update to the International Classification of
Diseases (ICD9-CM). The methods being used at Columbia-Presbyterian
Medical Center to reconcile its Medical Entities Dictionary and its
clinical database are discussed. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Cimino JJ, Clayton PD, Hripcsak G, Johnson SB. Knowledge-based
approaches to the maintenance of a large controlled medical terminology. J
Am Med Inform Assoc 1994 Jan-Feb;1(1):35-50. OBJECTIVE: Develop a
knowledge-based representation for a controlled terminology of clinical
information to facilitate creation, maintenance, and use of the
terminology. DESIGN: The Medical Entities Dictionary (MED) is a semantic
network, based on the Unified Medical Language System (UMLS), with a
directed acyclic graph to represent multiple hierarchies. Terms from four
hospital systems (laboratory, electrocardiography, medical records coding,
and pharmacy) were added as nodes in the network. Additional knowledge
about terms, added as semantic links, was used to assist in integration,
harmonization, and automated classification of disparate terminologies.
RESULTS: The MED contains 32,767 terms and is in active clinical use.
Automated classification was successfully applied to terms for laboratory
specimens, laboratory tests, and medications. One benefit of the approach
has been the automated inclusion of medications into multiple
pharmacologic and allergenic classes that were not present in the pharmacy
system. Another benefit has been the reduction of maintenance efforts by
90%. CONCLUSION: The MED is a hybrid of terminology and knowledge. It
provides domain coverage, synonymy, consistency of views, explicit
relationships, and multiple classification while preventing redundancy,
ambiguity (homonymy) and misclassification. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Cimino JJ, Hripcsak G, Johnson SB, Clayton PD. Designing an
introspective, multipurpose, controlled medical vocabulary. Proc Annu Symp
Comput Appl Med Care 1989:513-8. The medical vocabulary used in clinical
information systems must be more than a simple list of terms. We agree
that such a vocabulary must have synonymy, domain completeness, and
multiple classifications providing consistent views and explicit
relationships, while remaining unambiguous and non-redundant. We examine
the abilities of existing controlled vocabularies (ICD9-CM, SNOMED, MeSH,
CMIT, CPT4, COSTAR, HELP, DXPLAIN, and UMLS) to meet these goals and
propose an enhanced vocabulary structure based on a directed, acyclic
semantic net. This structure provides a representation which permits
introspection by the vocabulary maintenance system responsible for
providing a terminology which meets the seven requirements. The
vocabulary, called the Medical Entities Dictionary (MED), will serve a
variety of applications. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Cimino JJ, Hripcsak G, Johnson SB, Friedman C, Fink DJ, Clayton PD.
UMLS as knowledge base- a rule-based expert system approach to controlled
medical vocabulary management. Proc Annu Symp Comput Appl Med Care
1990:175-9. The National Library of Medicine is developing a Unified
Medical Language System (UMLS) which addresses the need for integration of
several large, nationally accepted vocabularies. This is important to the
clinical information system under development at the Columbia-Presbyterian
Medical Center (CPMC). The authors are using UMLS components as the core
of their effort to integrate existing local CPMC vocabularies which are
not among the source vocabularies of the UMLS. They are also using the
UMLS to build a knowledge base of vocabulary structure and content such
that logical rules can be developed to assist in the management of the
integrated vocabularies. At present, the UMLS Semantic Network is used to
organize terms which describe laboratory procedures. The authors have
developed a set of rules for identifying undesirable conditions in the
vocabulary. They have applied these rules to 526 laboratory test terms and
have found ten cases (2%) of definite redundancy and sixty-eight cases
(13%) of potential redundancy. The rules have also been used to organize
the terminology in new ways that facilitate its management. Using the UMLS
model as a vocabulary knowledge base allows the authors to apply an expert
system approach to vocabulary integration and management. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Evans DA, Cimino JJ, Hersh WR, Huff SM, Bell DS. Toward a
medical-concept representation language. The Canon Group. J Am Med Inform
Assoc 1994 May-Jun;1(3):207-17. The Canon Group is an informal
organization of medical informatics researchers who are working on the
problem of developing a deeper representation formalism for use in
exchanging data and developing applications. Individuals in the group
represent experts in such areas as knowledge representation and
computational linguistics, as well as in a variety of medical
subdisciplines. All share the view that current mechanisms for the
characterization of medical phenomena are either inadequate (limited or
rigid) or idiosyncratic (useful for a specific application but incapable
of being generalized or extended). The Group proposes to focus on the
design of a general schema for medical-language representation including
the specification of the resources and associated procedures required to
map language (including standard terminologies) into representations that
make all implicit relations visible, reveal hidden attributes, and
generally resolve ambiguous or vague references. The Group is proceeding
by examining large numbers of texts (records) in medical sub-domains to
identify candidate concepts and by attempting to develop general rules and
representations for elements such as attributes and values so that all
concepts may be expressed uniformly. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Fowler J, Buffone G, Moreau D. The architecture of a distributed
medical dictionary. Medinfo 1995;8(Pt 1):126-30. Exploiting high-speed
computer networks to provide a national medical information infrastructure
is a goal for medical informatics. The Distributed Medical Dictionary
under development at Baylor College of Medicine is a model for an
architecture that supports collaborative development of a distributed
online medical terminology knowledge-base. A prototype is described that
illustrates the concept. Issues that must be addressed by such a system
include high availability, acceptable response time, support for local
idiom, and control of vocabulary.</P>
<P>Humphreys BL. Comment on "Toward data standards for clinical nursing
information". J Am Med Inform Assoc 1994 Nov-Dec;1(6):472-4.</P>
<P>Levesque Y, LeBlanc AR, Maksud M. MD Concept: a model for integrating
medical knowledge. Proc Annu Symp Comput Appl Med Care 1994:252-6. Many
integrated clinical information systems depend on large knowledge bases
containing a dictionary of terms as well as specific information about
each term and the relationships between terms. We propose a knowledge base
model called MD Concept which is based on a semantic network and uses an
object-oriented paradigm and relational tables. A prototype has been
developed which integrates the Unified Medical Language System (UMLS) with
other databases including the Systematized Nomenclature of Medicine
(SNOMED II), the Diagnostic and Statistical Manual of Mental Disorders
(DSM-IIIR) and a pharmaceutical database. We demonstrate how a user can
easily navigate in this knowledge world using a browser. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Rada R. Maintaining thesauri and metathesauri. Int Classif 1990
;17(3-4):158-164. Maintaining a thesuarus is a time-consuming task which
should go hand-in-hand with the indexing of information and should be
supported by software. To connect different docuement databases their
respective thesauri should be related. The most straightforward way to
support this by computer is to map the terms of one thesaurus to those of
another. Such a mapping creates one kind of metathesaurus. As citation
systems are extended to include full-text on-line , a new thesaurus may be
used to index individual paragraphs of a document, and a metathesaurus may
apply to a universe of paragraphs. To illustrate these principles several
computer systems are described which help people maintain thesauri and
metathesauri. Particular success has been had by the National Library of
Medicine with its Medical Subject Headings and its Unified Medical
Language System. Copyright International Society for Knowledge
Organization.</P>
<P>Rosse C, Ben Said M, Eno KR, Brinkley JF. Enhancements of anatomical
information in UMLS knowledge sources. Proc Annu Symp Comput Appl Med Care
1995:873-7. Although anatomical terminology forms a part of biomedical
structured vocabularies, available sources lack the requisite granularity,
semantic types and relationships for comprehensively and consistently
representing anatomical concepts in machine readable form. Thoracic
angiology was selected as a proof of concept experiment for in depth
representation of symbolic information in gross anatomy through the
enhancement of semantic types, concepts and relationships in UMLS.
Provided the representation of concepts is comprehensive, hierarchies
generated with four types of simple relationships are capable of
displaying anatomical information from the systemic view point with
sufficient detail to meet the needs of applications in basic science
education and in the practice of surgical subspecialties. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Wigertz OB, Clayton PD, Hripcsak G, Linnarsson R. Knowledge
representation and data model to support medical knowledge base
transportability. In: Talmon JL, Fox J, editors. Knowledge based systems
in medicine: methods, applications and evaluation. Proceedings of the
Workshop System Engineering in Medicine; 1989 Mar 16-18; Maastricht,
Netherlands. Berlin: Springer-Verlag; 1991. p. 80-90. The authors discuss
the thesis that it is possible to design a data model and a representation
of the medical decision-making knowledge in a sufficiently high level and
modular format to ease transportability between institutions and systems.
They discuss some of the prerequisites of this uniform representation of
medical terms, medical data and medical logic. They discuss UMLS (unified
medical language system) and its metathesaurus. The possible impact of the
sharing of knowledge bases on the development and use of medical decision
support systems is also considered.</P><A
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<HR>
<UL>
<LI>
<UL>
<LI><STRONG><A name=3b>Vocabulary Standards, Servers, and Mapping
Methods</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Anderson CL, Hukill M, Wang W, Bangerter B, Kattelman M, Hartmann-Voss
K. A practical approach to structuring data in an integrated expert
system. Proc Annu Symp Comput Appl Med Care 1990:599-603. At the onset of
creating an expert system integrated into existing clinical information
systems, the need for a special data dictionary which could map to diverse
terminology in a variety of domains at a variety of health care delivery
sites was identified. Based upon research conducted on existing medical
nomenclatures, a methodology for structuring the expert system data
dictionary was produced. The dictionary is segmented into specific domains
(e.g. pharmacy, laboratory, etc.) as determined by traditional health care
specialties. Terms within each domain are categorized further with
guidance from working conventions commonly found within that specialty
(e.g. ICD-9-CM, CPT-4, etc.). Emphasis was placed on selecting protocols
consistent with those used in the Unified Medical Language System to
accommodate future translatability. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Chute CG, Cesnik B, van Bemmel JH. Medical data and knowledge
management by integrated medical workstations: summary and
recommendations. Int J Biomed Comput 1994 Jan;34(1-4):175-83. The health
care professional workstation will function as an interface between the
user and the patient data as well as an interface pertinent medical
knowledge. Appropriate knowledge focus will require the workstation to
recognize the concepts and structure of patient data, and understand the
scope and access methods of knowledge sources. Issues are organized around
five major themes: (i) structure, (ii) reliability and validation, (iii)
views, (iv) location, and (v) ethical and legal. Conventional database
representations can effectively address data structure and format
variations that will inevitably persist in local data stores. The
reliability of data and the validation of knowledge are critical issues
that may determine the ultimate utility of clinical workstations.
Alternative views of patient information and knowledge sources represent
the true power of an intelligent data portal, represented by a
well-designed clinical workstation. Both data and knowledge are optimally
represented in decentralized information networks, although the
confidentiality and ownership of this information must be respected.
Evolutionary progress toward consistent representations of knowledge and
patient data will be facilitated by the establishment of
self-documentation standards for the developers of data encoding systems
and knowledge sources, perhaps extended from the preliminary model
afforded by the Unified Medical Language System (UMLS).</P>
<P>Cimino JJ. Data storage and knowledge representation for clinical
workstations. Int J Biomed Comput 1994 Jan;34(1-4):185-94. The
representation of patient information for use in clinical workstations is
a complex problem. Ideally, it should be addressed in a way that allows
multiple uses of the data, including simple manual review, sharing and
pooling across institutions, and as input to knowledge-based decision
support systems. To a great extent, this means coding information with
controlled medical vocabularies, but it does not mean that all information
must be codable before workstations are feasible. This paper defines some
of the choices, both current and future, that are available to address the
needs of controlled medical vocabularies for representing data and
knowledge in clinical workstations and explores some of the implications
of those choices.</P>
<P>Cimino JJ, Barnett GO. Automated translation between medical
terminologies using semantic definitions. MD Comput 1990
Mar-Apr;7(2):104-9. Published erratum appears in MD Comput 1990
Jul-Aug;7(4):268. Automatic translation of medical terms from one
controlled vocabulary into another is essential to the integration of
diverse medical informatics systems. We have developed a strategy in which
medical terms are represented in a standard format that provides semantic
description of the terms. We demonstrate the representational power of our
method by showing that a subset of medical terms (procedures) from diverse
vocabularies can be described in this manner. We assess the potential
usefulness of our approach for facilitating automatic translation by
finding the closest match for MeSH cardiovascular procedures with ICD-9
procedures. Copyright 1990 Springer-Verlag.</P>
<P>Cimino JJ, Johnson SB, Hripcsak G, Sideli RV, Fink DJ, Friedman C,
Clayton PD. One year's experience with the Unified Medical Language System
(UMLS) in academia and patient care. Medinfo 1992;7(Pt 2):1501-5. The
first edition of the Unified Medical Language System (UMLS), released in
September 1990 by the National Library of Medicine consists of a
metathesaurus of 78862 interrelated terms and a semantic network for
categorizing these terms and representing additional relationships between
them. The integration of information systems at the Columbia-Presbyterian
Medical Center requires attention to the problem of reconciling the
diverse controlled vocabularies used by each system. One of the purposes
of the UMLS is to facilitate automatic methods for such reconciliation.
The authors have been exploring the suitability of the UMLS for various
aspects of the vocabulary management tasks, including vocabulary
organization, vocabulary representation and automated vocabulary
translation. The UMLS is demonstrated to have specific value for
vocabulary representation and translation; however, many areas are
identified where further development of its knowledge sources would be
useful.</P>
<P>France FH. Standards for nomenclature (HIS). In: Bakker AR, Ehlers CTh,
Bryant JR, Hammond WE, editors. Hospital information systems:
scope-design-architecture. Proceedings of the IMIA Working Conference;
1991 Sep 7-11; Gottingen, Germany. Amsterdam: North-Holland; 1992. p.
167-74. Uniform HISs which allow one to retrieve medical terms with the
same meaning are discussed. The ICD-10 (International Classification of
Diseases, 10th Revision) is expected to be published in 1993 by the World
Health Organisation (WHO), with an alphabetic index containing former
ICD-9 codes (conversion table). Each country has to decide when ICD-10
will be in use for hospitalized patients. Mapping extensions of ICD-9 to
ICD-10 will take some more time, as well as conversion tables to DSM III,
SNOMED, or MeSH, as performed by UMLS (Unified Medical Language System of
the National Library of Medicine-USA). ICD-9-CM is updated regularly in
the USA, but insufficient to describe laboratory tests, X-Rays procedures,
drugs; ICCS (International Classification of Clinical Services) contains
such information, complementary to ICD-9-CM. ICCS might be tested for
mapping other codes, as a kind of metacode, in order to detect differences
between national nomenclatures, when they exist. Up to now it remains
'Canadian-American' rather than 'international'. Standards for
nomenclature should also include rules for coding, as well as elements of
semantics in order to enable similar interpretation.</P>
<P>Houtchens BA, Allen A, Clemmer TP, Lindberg DA, Pedersen S.
Telemedicine protocols and standards: development and implementation. J
Med Syst 1995 Apr;19(2):93-119.</P>
<P>Humphreys BL, Hole WT, McCray AT, Fitzmaurice JM. Planned NLM/AHCPR
large-scale vocabulary test: using UMLS technology to determine the extent
to which controlled vocabularies cover terminology needed for health care
and public health. J Am Med Inform Assoc 1996 Jul-Aug;3(4):281-7. The
National Library of Medicine (NLM) and the Agency for Health Care Policy
and Research (AHCPR) are sponsoring a test to determine the extent to
which a combination of existing health-related terminologies covers
vocabulary needed in health information systems. The test vocabularies are
the 30 that are fully or partially represented in the 1996 edition of the
Unified Medical Language System (UMLS) Metathesaurus, plus three planned
additions: the portions of SNOMED International not in the 1996
Metathesaurus, the Read Clinical Classification, and the Logical
Observations Identifiers, Names, and Codes (LOINC) system. These
vocabularies are available to testers through a special interface to the
Internet-based UMLS Knowledge Source Server. The test will determine the
ability of the test vocabularies to serve as a source of controlled
vocabulary for health data systems and applications. It should provide the
basis for realistic resource estimates for developing and maintaining a
comprehensive "standard" health vocabulary that is based on existing
terminologies. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Masys DR. Of codes and keywords: standards for biomedical nomenclature.
Acad Med 1990 Oct;65(10):627-9.</P>
<P>McCormick KA, Lang N, Zielstorff R, Milholland DK, Saba V, Jacox A.
Toward standard classification schemes for nursing language:
recommendations of the American Nurses Association Steering Committee on
Databases to Support Clinical Nursing Practice. J Am Med Inform Assoc 1994
Nov-Dec;1(6):421-7. The American Nurses Association (ANA) Cabinet on
Nursing Practice mandated the formation of the Steering Committee on
Databases to Support Clinical Nursing Practice. The Committee has
established the process and the criteria by which to review and recommend
nursing classification schemes based on the ANA Nursing Process Standards
and elements contained in the Nursing Minimum Data Set (NMDS) for
inclusion of nursing data elements in national databases. Four
classification schemes have been recognized by the Committee for use in
national databases. These classification schemes have been forwarded to
the National Library of Medicine (NLM) for inclusion in the Unified
Medical Language System (UMLS) and to the International Council of Nurses
for the development of a proposed International Classification of Nursing
Practice. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Pretschner DP. Data analysis and information modelling: objects codes,
concepts. Radiat Prot Dosim 1995;57 (1-4):175-84. </P>
<P>Prokosch HU, Dudeck J, Michel A. Standards for data dictionaries (HIS).
In: Bakker AR, Ehlers CTh, Bryant JR, Hammond WE, editors. Hospital
information systems: scope-design-architecture. Proceedings of the IMIA
Working Conference; 1991 Sep 7-11; Gottingen, Germany. Netherlands:
North-Holland; 1992. p. 189-95. A controlled vocabulary is a basic
requirement in the development and implementation of HIS. A medical data
dictionary (MDD) has to provide a framework for such a controlled
vocabulary and additionally the possibility to define semantic
relationships and mappings to other MDDs. Several useful models for MDDs
have been developed in the last years. Among these the UMLS seems to be
the most comprehensive one. Unfortunately this project is still limited to
the US. In order to achieve one standard framework for MDD development,
researchers from Europe and all over the world will have to carefully
analyze the work which has already been done within UMLS and try to
finally agree to one common approach.</P>
<P>Prokosch HU, Kamm S, Wieczorek D, Dudeck J. Knowledge representation in
pharmacology. A possible application area for the Arden Syntax? Proc Annu
Symp Comput Appl Med Care 1991:243-7. In 1990 the Arden Syntax was
proposed as a first version of a standardized syntax for the
representation of medical knowledge. For the evaluation of the
practicability of this first release we have analyzed the medical and
pharmacological knowledge applied in the process of drug prescription. The
separation of declarative (e.g. in a semantic network) and procedural
knowledge is a basic issue of our research. We therefore propose to
further extend the Arden syntax with declarative knowledge representation
facilities. One way to do this may be the incorporation of a standardized
medical data dictionary (e.g. the UMLS Metathesaurus) which promotes the
representation of medical terms in a semantic network. Furthermore the
problem of 'institution-specific knowledge', which is especially important
for the issue of knowledge sharing between different institutions, is
analyzed based on examples of knowledge modules for monitoring drug
allergies and drug-drug-interactions. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Rocha RA, Beatriz MD, Huff SM. Automated translation between medical
vocabularies using a frame-based interlingua. Proc Annu Symp Comput Appl
Med Care 1993:690-4. The integration of clinical systems almost always
requires a translation phase, where vocabularies are compared and the
similar concepts are matched. The lack of standards in the area of medical
concept representation makes this task very difficult. The authors
describe the development of a frame-based application that automatically
translates terms found in one vocabulary to another. The application
implements an innovative scoring algorithm that ranks the best matches
using an exponential scale. Preliminary results and the comparison against
a manual process in the same domain are also discussed. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Rocha RA, Huff SM. Using digrams to map controlled medical
vocabularies. Proc Annu Symp Comput Appl Med Care 1994:172-6. A program
for matching between controlled medical vocabularies has been developed
which adopts methods used in the domain of Information Retrieval. This
program combines a stemmer based on fragments of words (digrams) with a
similarity function. The proposed stemmer did not require any knowledge
about word-formation rules and helped the identification of several kinds
of word variants. The adopted similarity function assigned the highest
score to the best candidate match in 99.0% of the cases. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Rocha RA, Huff SM, Haug PJ, Warner HR. Designing a controlled medical
vocabulary server: the VOSER project. Comput Biomed Res 1994
Dec;27(6):472-507. The authors describe their experience designing a
controlled medical vocabulary server created to support the exchange of
patient data and medical decision logic. The first section introduces
practical and theoretical premises that guided the design of the
vocabulary server. The second section describes a series of structures
needed to implement the proposed server, emphasizing their conformance to
the design premises. The third section introduces potential applications
that provide services to end users and also a group of tools necessary for
maintaining the server corpus. In the fourth section, the authors propose
an implementation strategy based on a common framework and on the
participation of groups from different health-related domains. Copyright
1994 Academic Press.</P>
<P>Walker DC, Walters RF. Developing a multilingual index to access
health-care terminologies. M Comput 1993 Sep;1(4):32-3, 36-42.</P>
<P>Walker DC, Walters RF, Cimino JJ, Dujols P, Li Ensheng, Giere W, Kiuchi
T, Lamberts H, Moore WG, Roger FH, Satomura Y, Stitt FW.
Internationalization of health care terminology. Medinfo 1992;7(Pt
2):1444-51. The Unified Medical Language System (UMLS) of the National
Library of Medicine (NLM) provides a terminology interface for biomedical
resources in the USA. A project to develop a multinational terminology
resource could effectively extend the existing thesaurus of the UMLS, and
help the internationalization of medical information. What the UMLS is at
this moment, is summarized in this paper. Some terminologies with
'terminology browsers' are briefly described. The formation of a more
encompassing multilingual master index to access various terminologies and
their 'browsers' is advocated. An international body to initiate and
coordinate any such project would be needed.</P>
<P>Zeng Q, Cimino JJ. Mapping medical vocabularies to the Unified Medical
Language System. Proc AMIA Fall Symp 1996:105-9. This paper presents our
work in automated mapping of medical vocabularies to the National Library
of Medicine's Unified Medical Language System (UMLS). We used the UMLS
Knowledge Source (KS) tool to map terms from several sources to UMLS
Metathesaurus concepts. We compared performance of the KS tools with our
own Minimal Representable Units Method (MRUM). The KS tools were able to
map terms from 13% to 54% of the time, depending on the term set and the
KS options used. Our MRUM method mapped between 96% and 99% of the terms.
Based on our experience, we believe that questions remain about the best
method by which the UMLS can be used to achieve automated term
translation. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Zielstorff RD, Lang NM, Saba VK, McCormick KA, Milholland DK. Toward a
uniform language for nursing in the US: work of the American Nurses
Association Steering Committee on databases to support clinical practice.
Medinfo 1995;8(Pt 2):1362-6. This paper reports on the work of the
American Nurses Association Steering Committee on Databases to Support
Clinical Practice, in existence since 1989. Responding to its broad
charges, the Steering Committee has laid down the foundations for its work
in declaring the nursing process as the framework for nursing data in
database systems, and in endorsing the Nursing Minimum Data Set as the set
of minimum elements for any system designed to carry health-related data
that reflects nursing care. In addition, the Steering Committee has begun
initiatives to: 1) promote the inclusion of nursing-related data in large
health-related databases, and 2) develop a Uniform Language for nursing
through a phased approach. The Steering Committee also works directly with
the International Council of Nurses to promote the inclusion of nursing
data in internationally used classification systems and to develop an
international language that describes nursing care.</P><A
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<HR>
<UL>
<LI>
<UL>
<LI><STRONG><A name=3c>Knowledge Acquisition and Concept
Discovery</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Burgun A, Bodenreider O, Denier P, Delamarre D, Botti G, Lukacs B,
Mayeux D, Bremond M, Kohler F, Fieschi M, et al. Knowledge acquisition
from the UMLS sources: application to the description of surgical
procedures. Medinfo 1995;8(1):75-9. The re-usability of lexicons and
knowledge in medicine is a crucial challenge. The Unified Medical Language
System (UMLS) project has attempted to provide a repository of concepts,
semantically categorized for biomedical domain. This paper describes some
results about the relevance of UMLS structures for specific purposes. We
have focused on the description of surgical procedures. Discussion
concerns synonymy of terms, granularity of concepts, and ontology. A
preliminary work on the exploitation of interconcept links by a
computerized application reveals a heterogeneous implementation of those
relationships. However, the UMLS provides a powerful knowledge base for
developers.</P>
<P>Burgun A, Botti G, Lukacs B, Mayeux D, Seka LP, Delamarre D, Bremond M,
Kohler F, Fieschi M, Le Beux P. A system that facilitates the orientation
within procedure nomenclatures through a semantic approach. Med Inf (Lond)
1994 Oct-Dec;19(4):297-310.</P>
<P>Burgun A, Delamarre D, Botti G, Lukacs B, Mayeux D, Bremond M, Kohler
F, Fieschi M, Le Beux P. Designing a sub-set of the UMLS knowledge base
applied to a clinical domain: methods and evaluation. Proc Annu Symp
Comput Appl Med Care 1994:968. The UMLS is a complex collection of
interconnected biomedical concepts derived from standard nomenclatures.
Designing a specific subset of the UMLS knowledge base relevant to a
medical domain is a prerequisite for the development of specialized
applications based on UMLS. We have developed a method based on the
selection of the appropriate terms in original nomenclatures and the
capture of a set of UMLS terms that are linked to them in the network to a
certain degree. We have experimented it as the foundation for a concept
base applied to urology. Results depend on the exhaustiveness of the
relationships between the Meta-1 concepts. A preliminary analysis of the
sub-base reveals that some adaptations of vocabulary and ontology are
required for clinical applications. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Gangemi A, Galanti M, Galeazzi E, Rossi Mori A. Beyond UMLS:
computational semantics for medical records. Medinfo 1992;7(Pt 1):703-8.
Computational semantics is a promising approach for effective processing
of clinical data, integrating medical record, information retrieval
applications, statistical databases and knowledge based systems. The
authors introduce 'semiotic codes', a generalization of medical language
and artificial coding systems, and describe their power by a scale: (C1)
non-combinatorial Codes (icons); (C2) combinatorial Codes, with finite set
of signs (conventional coding systems); (C3) combinatorial Codes, with
potentially infinite set of signs (combinatorial expressions); (C4)
combinatorial Codes, with calculable synonymy (formal languages); (C5)
creative Codes with unpredictable synonymy and homonymy (natural
languages). In order to convert each potential Semiotic Code to another,
one needs a system of class C4, that is computationally 'more powerful'
than any other. It is based on formal expressions, allowing to compare
definitions of concepts to decide their equivalence. It acts as an
interlingua to represent medical concepts in the computer, in a neutral
way with respect to other semiotic codes and applications.</P>
<P>Hardy B, Burgun A, Le Beux P. Accessing to knowledge base terms using
UMLS concepts. In: Brender J, Christensen JP, Scherrer JR, McNair P,
editors. Medical Informatics Europe '96: Human facets in information
technologies. Washington: IOS Press; 1996. p. 164-8. (Studies in health
technology and informatics; 34). This paper presents the first phase of a
project of a terminology server based on the UMLS project and using both
lexical mapping and conceptual relations. The choice of tools has been to
build a user to data knowledge base using the PERL language associated the
World Wide Web technology and relational data base (ORACLE <SUP><FONT
size=1>tm</FONT></SUP>).</P>
<P>Hersh WR, Campbell EH, Evans DA, Brownlow ND. Empirical, automated
vocabulary discovery using large text corpora and advanced natural
language processing tools. Proc AMIA Fall Symp 1996:159-63. A major
impediment to the full benefit of electronic medical records is the lack
of a comprehensive clinical vocabulary. Most existing vocabularies do not
allow the full expressiveness of clinical diagnoses and findings that are
often qualified by modifiers relating to severity, acuity, and temporal
factors. One reason for the lack of expressivity is the inability of
traditional manual construction techniques to identify the diversity of
language used by clinicians. This study used advanced natural language
processing tools to identify terminology in a clinical findings domain,
compare its coverage with the UMLS Metathesaurus, and quantify the effort
required to discover the additional terminology. It was found that
substantial amounts of phrases and individual modifiers were not present
in the UMLS Metathesaurus and that modest effort in human time and
computer processing were needed to obtain the larger quantity of terms.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Nelson SA, Olson NE, Fuller L, Tuttle MS, Cole WG, Sherertz DD.
Identifying concepts in medical knowledge. Medinfo 1995;8(Pt 1):33-6. The
barrier word method of identifying nominal phrases in text, using a very
long barrier word list, was evaluated in two different sets of text. In a
sample of 10 paragraphs from the Medical Knowledge Self-Assessment Program
of the American College of Physicians, the yield of nominal phrases as a
percent of total chunks isolated was 66%. Some 500,000 chunks were
isolated from Principles and Practice of Oncology (PPO). 38% of these
chunk-occurrences were of chunks which matched to 10,000 concept names in
Meta-1.4, the most recent version of the UMLS Metathesaurus. 50 paragraphs
from PPO were chosen at random. Co-occurrences of concepts in those
paragraphs were reviewed. 42 of the paragraphs had unique or infrequently
occurring co-occurrences which described closely the major thrust of the
paragraph.</P>
<P>Nelson SJ, Cole WG, Tuttle MS, Olson NE, Sherertz DD. Recognizing new
medical knowledge computationally. Proc Annu Symp Comput Appl Med Care
1993:409-13. Can new medical knowledge be recognized computationally? We
know knowledge is changing, and our knowledge-based systems will need to
accommodate that change in knowledge on a regular basis if they are to
stay successful. Computational recognition of these changes seems
desirable. It is unlikely that low level objects in the computational
universe, bits and characters, will change much over time, higher level
objects of language, where meaning begins to emerge, may show change. An
analysis of ten arbitrarily selected paragraphs from the Medical Knowledge
Self-Assessment Program of the American College of Physicians was used as
a test bed for nominal phrase recognition. While there were words not
known to Meta-1.2, only 8 of the 32 concepts new to the primary author
were pointed to by new words. Use of a barrier word method was successful
in identifying 23 of the 32 new concepts. Use of co-occurrence (in
sentences) of putative nominal phrases may reduce the amount of human
effort involved in recognizing the emergence of new relationships.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Rindflesch TC, Aronson AR. Ambiguity resolution while mapping free text
to the UMLS Metathesaurus. Proc Annu Symp Comput Appl Med Care 1994:240-4.
We propose a method for resolving ambiguities encountered when mapping
free text to the UMLS Metathesaurus. Much of the research in medical
informatics involves the manipulation of free text. The Metathesaurus
contains extensive information which supports solutions to problems
encountered while processing such text. After discussing the process of
mapping free text to the Metathesaurus and describing the ambiguities
which are often the result of such mapping, we provide examples of rules
designed to eliminate mapping ambiguities. These rules refer to the
context in which the ambiguity occurs and crucially depend on semantic
types obtained from the Metathesaurus. We have conducted a preliminary
test of the methodology and the results obtained indicate that the rules
successfully resolve ambiguity around 80% of the time. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Sneiderman CA, Rindflesch TC, Aronson AR. Finding the findings:
identification of findings in medical literature using restricted natural
language processing. Proc AMIA Fall Symp 1996:239-43. The ability to
search the biomedical literature based on findings would provide enhanced
access to information. We describe a computer program called FINDX which
relies on the UMLS Metathesaurus and restricted natural language
processing to identify findings in free text. Such identification can
serve as a filtering mechanism while selecting relevant papers. After
discussing the salient characteristics of findings on which FINDX depends,
we report on the results of an experiment in which we tested the program
on a set of MEDLINE abstracts pertaining to the diagnosis of Parkinson
Disease. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG>Data Creation</STRONG><BR>
<UL>
<LI><STRONG><A name=3d>Clinical Data</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Cimino JJ. Use of the Unified Medical Language System in patient care
at the Columbia-Presbyterian Medical Center. Methods Inf Med 1995
Mar;34(1-2):158-64. The Unified Medical Language System (UMLS) project at
the United States National Library of Medicine contains and organizes a
large number of terms from controlled medical vocabularies. This study
examines the suitability of the UMLS for representing patient care
information as it exists in the Columbia-Presbyterian Medical Center
(CPMC) clinical in formation system. Comparisons were made between the
semantic types, semantic relations and medical concepts of the UMLS and
the data model entities, semantic classes, semantic relations and concepts
in the CPMC system. Results of the comparison demonstrate that the UMLS
structural model is appropriate for representing CPMC vocabularies and
patient data and that the UMLS concepts provide excellent coverage of CPMC
concepts in many areas. Recommendations are made for enhancing UMLS
structure to provide additional coverage of the CPMC model. It is
concluded that content expansion to provide better coverage of clinical
terminology is possible within the current UMLS model.</P>
<P>Cimino JJ, Barnett GO. The physician's workstation: recording a
physical examination using a controlled vocabulary. Proc Annu Symp Comput
Appl Med Care 1987:287-91. A system has been developed which runs on
MS-DOS personal computers and serves as an experimental model of a
physician's workstation. The program provides an interface to a controlled
vocabulary which allows rapid selection of appropriate terms and modifiers
for entry of clinical information. Because it captures patient
descriptions, it has the ability to serve as an intermediary between the
physician and computer-based medical knowledge resources. At present, the
vocabulary permits rapid, reliable representation of cardiac physical
examination findings. Copyright 1987 IEEE. Reprinted, with permission.</P>
<P>Lindberg DA, Humphreys BL. The Unified Medical Language System (UMLS)
and computer-based patient records. In: Ball MJ, Collen MF, editors.
Aspects of the computer-based patient record. New York: Springer-Verlag;
1992. p. 165-75.</P>
<P>Lowe HJ. Image Engine: an object-oriented multimedia database for
storing, retrieving and sharing medical images and text. Proc Annu Symp
Comput Appl Med Care 1993:839-43. This paper describes Image Engine, an
object-oriented, microcomputer-based, multimedia database designed to
facilitate the storage and retrieval of digitized biomedical still images,
video, and text using inexpensive desktop computers. The current prototype
runs on Apple Macintosh computers and allows network database access via
peer to peer file sharing protocols. Image Engine supports both free text
and controlled vocabulary indexing of multimedia objects. The latter is
implemented using the TView thesaurus model developed by the author. The
current prototype of Image Engine uses the National Library of Medicine's
Medical Subject Headings (MeSH) vocabulary (with UMLS Meta-1 extensions)
as its indexing thesaurus. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Lowe HJ, Buchanan BG, Cooper GF, Vries JK. Building a medical
multimedia database system to integrate clinical information: an
application of high-performance computing and communications technology.
Bull Med Libr Assoc 1995 Jan;83(1):57-64. The rapid growth of
diagnostic-imaging technologies over the past two decades has dramatically
increased the amount of nontextual data generated in clinical medicine.
The architecture of traditional, text-oriented, clinical information
systems has made the integration of digitized clinical images with the
patient record problematic. Systems for the classification, retrieval, and
integration of clinical images are in their infancy. Recent advances in
high-performance computing, imaging, and networking technology now make it
technologically and economically feasible to develop an integrated,
multimedia, electronic patient record. As part of The National Library of
Medicine's Biomedical Applications of High-Performance Computing and
Communications program, we plan to develop Image Engine, a prototype
microcomputer-based system for the storage, retrieval, integration, and
sharing of a wide range of clinically important digital images. Images
stored in the Image Engine database will be indexed and organized using
the Unified Medical Language System Metathesaurus and will be dynamically
linked to data in a text-based, clinical information system. We will
evaluate Image Engine by initially implementing it in three clinical
domains (oncology, gastroenterology, and clinical pathology) at the
University of Pittsburgh Medical Center. Copyright by and reprinted with
permission of the Medical Library Association.</P>
<P>Stitt FW. The problem-oriented medical synopsis: coding, indexing, and
classification sub-model. Proc Annu Symp Comput Appl Med Care 1994:964. A
clinical information system consists of four major components: the
clinical database, decision support, data analysis (including outcomes),
and the development system. We have created such a system using generally
available database methodology. The system is documented using a
conceptual model, a physical model, and sub-models for individual
components. A key sub-model of the clinical database, for record-keeping,
has been defined for coding, indexing, and classification of the medical
narrative typically encountered in medical records. We describe an
approach to the development of the coding component that results in a
hybrid system for recording information, locating indexed information, and
summarizing it for analysis of outcomes. These are based on a primary term
list--the problem glossary; SNOMed--the Systematized Nomenclature of
Medicine (3rd. edition); and ICD-9-CM. The relationship with the UMLS is
also discussed. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Stitt FW. A standards-based clinical information system for HIV/AIDS.
Medinfo 1995;8(Pt 1):402. Objective: To create a clinical data repository
to interface the Veteran's Administration (VA) Decentralized Hospital
Computer Program (DHCP) and a departmental clinical information system for
the management of HIV patients. This system supports record-keeping,
decision-making, reporting, and analysis. The database development was
designed to overcome two impediments to successful implementations of
clinical databases: (i) lack of a standard reference data model, and; (ii)
lack of a universal standard for medical concept representation.
Background: Health Level Seven (HL7) is a standard protocol that specifies
the implementation of interfaces between two computer applications (sender
and receiver) from different vendors or sources of electronic data
exchange in the health care environment. This eliminates or substantially
reduces the custom interface programming and program maintenance that
would otherwise be required. HL7 defines the data to be exchanged, the
timing of the interchange, and the communication of errors to the
application. The formats are generic in nature and must be configured to
meet the needs of the two applications involved. The standard conceptually
operates at the seventh level of the ISO model for Open Systems
Interconnection (OSI). The OSI simply defines the data elements that are
exchanged as abstract messages, and does not prescribe the exact bit
stream of the messages that flow over the network. Lower level network
software developed according to the OSI model may be used to encode and
decode the actual bit stream. The OSI protocols are not universally
implemented and, therefore, a set of encoding rules for defining the exact
representation of a message must be specified. The VA has created an HL7
module to assist DHCP applications in exchanging health care information
with other applications using the HL7 protocol. The DHCP HL7 module
consists of a set of utility routines and files that provide a generic
interface to the HL7 protocol for all DHCP applications. Setting: The VA's
DHCP core modules are in standard use at 169 hospitals, and the role of
the VA system in health care delivery has been discussed elsewhere. This
development was performed at the Miami VA Medical Center Special
Immunology Unit, where a database was created for an HIV patient registry
in 1987. Over 2,300 patients have been entered into a database that
supports a problem-oriented summary of the patient's clinical record. The
interface to the VA DHCP was designed and implemented to capture
information from the patient treatment file, pharmacy, laboratory,
radiology, and other modules. Results: We obtained a suite of programs for
implementing the HL7 encoding rules from Columbia-Presbyterian Medical
Center in New York, written in ANSI C. This toolkit isolates our
application programs from the details of the HL7 encoding rules, and
allows them to deal with abstract messages and the programming level.
While HL7 has become a standard for healthcare message exchange, SQL
(Structured Query Language) is the standard for database definition, data
manipulation, and query. The target database provides clinical workstation
functionality. Medical concepts are encoded using a preferred terminology
derived from over 15 sources that include the Unified Medical Language
System and SNOMed International.</P>
<P>Trace D, Naeymi-Rad F, Almeida FD, Moidu K, Haines D. A longitudinal
medical record (IMR). Proc Annu Symp Comput Appl Med Care 1993:911. The
Intelligent Medical Record (IMR) is currently being used in patient care
activities at Norwalk Hospital in Norw alk, CT, and at Cook County
Hospital in Chicago, IL. IMR has evolved into a multi-encounter patient
record, stored in a multi-user database management system. The graphical
user interface is designed to support physician efforts to capture patient
data, c reate progress notes, and produce a longitudinal medical record.
The authors describe the program's major components, including its
multi-encounter knowledge management system, problem list, progress notes,
point-of-entry query, and interface to UMLS. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Wagner MM. An automatic indexing method for medical documents. Proc
Annu Symp Comput Appl Med Care 1991:1011-7. This paper describes
MetaIndex, an automatic indexing program that creates symbolic
representations of documents for the purpose of document retrieval.
MetaIndex uses a simple transition network parser to recognize a language
that is derived from the set of main concepts in the Unified Medical
Language System Metathesaurus (Meta-1). MetaIndex uses a hierarchy of
medical concepts, also derived from Meta-1, to represent the content of
documents. The goal of this approach is to improve document retrieval
performance by better representation of documents. An evaluation method is
described, and the performance of MetaIndex on the task of indexing the
Slice of Life medical image collection is reported. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Wagner MM, Cooper GF. Evaluation of a Meta-1-based automatic indexing
method for medical documents. Comput Biomed Res 1992 Aug;25(4):336-50.
This paper describes MetaIndex, an automatic indexing program that creates
symbolic representations of documents for the purpose of document
retrieval. MetaIndex uses a simple transition network parser to recognize
a language that is derived from the set of main concepts in the Unified
Medical Language System Metathesaurus (Meta-1). MetaIndex uses a hierarchy
of medical concepts, also derived from Meta-1, to represent the content of
documents. The goal of this approach is to improve document retrieval
performance by better representation of documents. An evaluation method is
described, and the performance of MetaIndex on the task of indexing the
Slice of Life medical image collection is reported. Copyright 1992
Academic Press.</P><A
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<HR>
<UL>
<LI>
<UL>
<LI><STRONG><A name=3e>Curricula and Faculty
Interests</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Breene M, Jasmin R, Eisner J. Computer-based curriculum analysis. A
customized approach using external standards and the UMLS. Proc Annu Symp
Comput Appl Med Care 1993:919. This article describes the beta test stage
of the first software product developed by The American Association of
Dental Schools (AADS) Curriculum Database Consortium, which is known as
CATs (Curriculum Analysis Tools). The consortium wanted to develop a
software tool that could adapt to the special circumstances of each of the
fifty Dental Schools and Allied Dental Programs, while accurately and
comprehensively representing their curricula. The product has satisfied
the principle requirements for user customization, cross-referencing to
external standards, and content searching by keyword using the UMLS. The
product provides an intuitive method of curriculum analysis with powerful
tools for viewing and interpreting the results. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Clyman SG. UMLS linked to a system for authoring simulations used in
evaluation of physicians. Proc Annu Symp Comput Appl Med Care 1993:921.
The National Board of Medical Examiners (NBME) develops examinations used
in licensing physicians in the United States. To complement existing
multiple-choice examinations, NBME has developed and is studying uncued,
dynamic, computer-based simulations (CBX) of the patient care environment.
In CBX, physicians type free-text orders for diagnostic studies,
procedures , consultants, medications, and other therapies. As simulated
time passes, patient conditions evolve in response to physician management
decisions; multiple outcomes are possible. One impediment to widespread
use of CBX is the technical expertise, time, a nd cost associated with it.
A new case authoring system called SEEDS (Simulation Environment
Engineering and Development System) will increase the efficiency of this
process. The National Library of Medicine's Unified Medical Language
System (UMLS) is use d in the development of SEEDS to link UMLS and CBX
terms and concepts. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Eisner J. Curriculum Analysis Tools (CATs). A cooperative approach to
the design of curriculum databases. Proc Annu Symp Comput Appl Med Care
1993:766-70. In 1990, a small group of dental schools agreed to pool their
resources and cooperate in the design and programming of curriculum
analysis software. After two and one-half years, the consortium had grown
to include more than 50 institutions. Its efforts have been endorsed by
the American Association of Dental Schools, and it is now beta testing its
first software product, known as Curriculum Analysis Tools (CATs). The
process by which the software has been developed, as well as its current
design, offers a unique blend of flexibility and creativity, which could
perhaps be adopted by other health professionals. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Eisner J. Multi-national, multi-lingual, multi-professional CATs:
(Curriculum Analysis Tools). Medinfo 1995;8(Pt 2):1706. A consortium of
dental schools and allied dental programs was established in 1991 with the
expressed purpose of creating a curriculum database program that was
end-user modifiable. In April of 1994, a beta version (Beta 2.5 written in
FoxPro(TM) 2.5) of the software CATs, an acronym for Curriculum Analysis
Tools, was released for use by over 30 of the consortium's 60 member
institutions, while the remainder either waited for the Macintosh (TM) or
Windows (TM) versions of the program or were simply not ready to begin an
institutional curriculum analysis project. Shortly after this release, the
design specifications were rewritten based on a thorough critique of the
Beta 2.5 design and coding structures and user feedback. The result was
Beta 3.0 which has been designed to accommodate any health professions
curriculum, in any country that uses English or French as one of its
languages. Given the program's extensive use of screen generation tools,
it was quite easy to offer screen displays in a second language. As more
languages become available as part of the Unified Medical Language System,
used to document curriculum content, the program's design will allow their
incorporation. When the software arrives at a new institution, the choice
of language and health profession will have been preselected, leaving the
Curriculum Database Manager to identify the country where the member
institution is located. With these 'macro' end-user decisions completed,
the database manager can turn to a more specific set of end-user questions
including: 1) will the curriculum view selected for analysis be created by
the course directors (provider entry of structured course outlines) or by
the students (consumer entry of class session summaries)?; 2) which
elements within the provided course outline or class session modules will
be used?; 3) which, if any, internal curriculum validation measures will
be in cluded?; and 4) which, if any, external validation measures will be
included. External measures can include accreditation standards,
entry-level practitioner competencies, an index of learning behaviors, an
index of discipline integration, or others defined by the institution.
When data entry, which is secure to the course level, is complete users
may choose to browse a variety of graphic representations of their
curriculum, or either preview or print a variety of reports that offer
more detail about the content and adequacy of their curriculum. The
progress of all data entry can be monitored by the database manager over
the course of an academic year, and all reports contain extensive missing
data reports to ensure that the user knows whether they are studying
complete or partial data. Institutions using the beta version of the
program have reported considerable satisfaction with its functionality and
have also offered a variety of design and interface enhancements. The
anticipated release date for Curriculum Analysis Tools (CATs) is the first
quarter of 1995.</P>
<P>Fowler J, Wheeler DA, Camerino PW, Bat O, Burch PE. Development of a
faculty research interest resource. Proc AMIA Fall Symp 1996:363-72. We
have developed a faculty research interests resource by "mining" MEDLINE
for relationships that are no t directly queryable through the normal
MEDLINE schema. Faculty citations are retrieved and World-Wide Web pages
built to interconnect authors, their citations, and the MeSH terms that
have been assigned to these citations. The design and development of t he
resource are discussed and examples of the results illustrated. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Kanter SL. Using the UMLS to represent medical curriculum content. Proc
Annu Symp Comput Appl Med Care 1993:762-5. Recent innovations in medical
education have highlighted the need for faculty involved with the
curriculum to carefully examine curricular content with goals of detecting
omissions and unwanted redundancies of subject matter, adding and
integrating new content, and deleting old content. A number of medical
schools have attempted to deal with these issues by developing a database
of curricular content information, most often using faculty- or
student-selected keywords to represent each unit of instruction. However,
several problems have been identified with this method, and achieving the
goals mentioned above remains a formidable task. This paper outlines an
alternative method that uses the resources of the UMLS to characterize a
medical concept by the semantic types of its co-occurring terms. This
approach can facilitate achievement of the aforementioned goals. Copyright
by and reprinted with permission of the American Medical Informatics
Association. </P>
<P>Kanter SL, Miller RA, Tan M, Schwartz J. Using POSTDOC to recognize
biomedical concepts in medical school curricular documents. Bull Med Libr
Assoc 1994 Jul;82(3):283-7. Recognition of the biomedical concepts in a
document is prerequisite to further processing of the document: medical
educators examine curricular documents to discover the coverage of certain
topics, detect unwanted redundancies, integrate new content, and delete
old content; and clinicians are concerned with terms in patient medical
records for purposes ranging from creation of an electronic medical record
to identification of medical literature relevant to a particular case.
POSTDOC (POSTprocessor of DOCuments) is a computer application that (1)
accepts as input a free-text, ASCII-formatted document and uses the
Unified Medical Language System (UMLS) Metathesaurus to recognize relevant
main concept terms; (2) provides term co-occurrence data and thus is able
to identify potentially increasing correlations among concepts within the
document; and (3) retrieves references from MEDLINE files based on user
identification of relevant subjects. This paper describes a formative
evaluation of POSTDOC's ability to recognize UMLS Metathesaurus biomedical
concepts in medical school lecture outlines. The precision and recall
varied over a wide range and were deemed not yet acceptable for automated
creation of a database of concepts from curricular documents. However,
results were good enough to warrant further study and continued system
development. Copyright by and reprinted with permission of the Medical
Library Association.</P>
<P>Zucker J, Chase H, Molholt P, Bean C, Kahn RM. A comprehensive strategy
for designing a web-based medical curriculum. Proc AMIA Fall Symp
1996:41-5. In preparing for a full featured online curriculum, it is
necessary to develop scaleable strategies for software design that will
support the pedagogical goals of the curriculum and which will address the
issues of acquisition and updating of materials, of robust content-based
linking, and of integration of the online materials into other methods of
learning. A complete online curriculum, as distinct from an individual
computerized module, must provide dynamic updating of both content and
structure and an easy pathway from the professor's notes to the finished
online product. At the College of Physicians and Surgeons, we are
developing such strategies including a scripted text conversion process
that uses the Hypertext Markup Language (HTML) as structural markup rather
than as display markup, automated linking by the use of relational
databases and the Unified Medical Language System (UMLS), integration of
text, images, and multimedia along with interface designs which promote
multiple contexts and collaborative study. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG>Natural Language Processing, Indexing and
Retrieval</STRONG><BR>
<UL>
<LI><STRONG><A name=3f>NLP Methods and
Algorithms</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Baud RH, Rassinoux A-M, Lovis C, Wagner J, Griesser V, Michel P-A,
Scherrer J-R. Knowledge sources for natural language processing. Proc AMIA
Fall Symp 1996:70-4. This paper aims at reviewing the problem of feeding
Natural Language Processing (NLP) too ls with convenient linguistic
knowledge in the medical domain. A syntactic approach lacks the potential
to solve a number of typical situations with ambiguities and is clearly
insufficient for quality treatment of natural language. On the other hand,
a co nceptual approach relies on some modelling of the domain, of which
the elaboration is a long-term process and where the ultimate solutions
are far from being recognised and universally accepted. In-between is the
beauty of the compromise. How can we signi ficantly improve the coverage
of linguistic knowledge in the years to come? Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Evans DA, Brownlow ND, Hersh WR, Campbell EM. Automating concept
identification in the eletronic medical record: an experiment in
extracting dosage information. Proc AMIA Fall Symp 1996:388-92. We discuss
the development and evaluation of an automated procedure for extracting
drug-dosage information from clinical narratives. The process was
developed rapidly using existing technology and resources, including
categories of terms from UMLS96. Evaluations over a large training and
smaller test set of medical records demonstrate an approximately 80% rate
of exact and partial matches on target phrases, with few false positives
and a modest rate of false negatives. The results suggest a strategy for
automating general concept identification in electronic medical records.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Evans DA, Chute CG, Handerson SK, Yang Y, Monarch IA, Hersh WR. 'Latent
semantics' as a basis for managing variation in medical terminologies.
Medinfo 1992;7(Pt 2):1462-8. The authors are exploiting a version of
latent semantic indexing as a general solution to the problem of managing
language variation. They treat medical terms as the 'documents' to be
retrieved by natural-language expressions of concepts, taken as 'queries'.
In experiments, they have focused on (1) establishing a basis for the
decomposition of concepts (terms) by lexical items and (2) exploiting
existing medical thesauri to create Lexical-Item x Term spaces. They have
demonstrated the ability to interpret natural-language statements of
medical findings in multiple medical terminologies simultaneously (e.g.
INTERNIST-I/QMR, PTXT, and NLM/UMLS META-1 vocabularies) and also to
derive concept-relation spaces from collections of terms in the NLM/UMLS
Metathesaurus (META-1). The power of this approach is that it does not
depend on detailed semantic representations or on word-for-word
correspondences among terms and that multiple vocabularies can be
represented side-by-side.</P>
<P>Johnson SB, Aguirre A, Peng P, Cimino J. Interpreting natural language
queries using the UMLS. Proc Annu Symp Comput Appl Med Care 1993:294-8.
This paper describes AQUA (A QUery Analyzer), the natural language front
end of a prototype information retrieval system. AQUA translates a user's
natural language query into a representation in the Conceptual Graph
formalism. The graph is then used by subsequent components to search
various resources such as databases of the medical literature. The focus
of the parsing method is on semantics rather than syntax, with semantic
restrictions being provided by the UMLS Semantic Net. The intent of the
approach is to provide a method that can be emulated easily in
applications that require simple natural language interfaces. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Joubert M, Fieschi M, Robert JJ. A conceptual model for information
retrieval with UMLS. Proc Annu Symp Comput Appl Med Care 1993:715-9.
Information retrieval in large information databases is a
non-deterministic process which needs a sequence of search steps
generally. One of the main problems to which the end-users are faced is to
parse efficiently their questions into the query language that the
computer systems allow. Conceptual graphs were initially designed for
natural language analysis and understanding. Due to their closeness to
semantic networks, their expressiveness is powerful enough to be applied
to knowledge representation and use by computer systems. This work
demonstrates that conceptual graphs are a suitable means to model the
end-users queries on the basis of the thesaurus and the semantic network
of the UMLS project. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Joubert M, Fieschi M, Robert JJ, Tafazzoli A. Users conceptual views on
medical information databases. Int J Biomed Comput 1994 Oct;37(2):93-104.
As information databases we consider all the kinds of information
repositories that are handled by computer systems. When querying very
large information databases, the end-users are often faced with the
problem to parse their questions efficiently into the query languages of
the computer systems. Conceptual graphs were initially designed for
natural language analysis and understanding. Due to their closeness to
semantic networks, their expressiveness is powerful enough to be applied
to knowledge representation and use by computer systems. This work
demonstrates that conceptual graphs are a suitable means to model both the
information in patient databases and the queries to these databases, and
that operations on graphs can compute the pattern matching process needed
to provide the answers. A prototype that exploits this model is presented.
Experiments have been made with the material furnished by the Unified
Medical Language System project (version 2, 1992) of the National Library
of Medicine, USA.</P>
<P>Joubert M, Robert J-J, Miton F, Fieschi M. The project ARIANE:
conceptual queries to information databases. Proc AMIA Fall Symp
1996:378-82. As information databases we consider all the collections of
data records indexed by key-words, stored and delivered by computer
systems. In previous research works we demonstrated the interest to design
a conceptual model, in the conceptual graphs formalism, and to implement a
computational model for information retrieval in large information
databases. These models are based on the UMLS knowledge sources. This
paper reminds briefly these models and describes tests done in querying a
patients database and a bibliographical database. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Lamiell JM, Wojcik ZM, Isaacks J. Computer auditing of surgical
operative reports written in English. Proc Annu Symp Comput Appl Med Care
1993:269-73. We developed a script-based scheme for automated auditing of
natural language surgical operative reports. Suitable operations
(appendectomy and breast biopsy) were selected, then audit criteria and
operation scripts conforming with our audit criteria were developed. Our
LISP parser was context and expectation sensitive. Parsed sentences were
represented by semigraph structures and placed in a textual database to
improve efficiency. Sentence ambiguities were resolved by matching the
narrative textual database to the script textual database and employing
the Uniform Medical Language System (UMLS) Knowledge Sources. All audit
criteria questions were successfully answered for typical operative
reports by matching parsed audit questions to the textual database.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>McCray AT. Extending a natural language parser with UMLS knowledge.
Proc Annu Symp Comput Appl Med Care 1991:194-8. Over the past several
years our research efforts have been directed toward the identification of
natural language processing methods and techniques for improving access to
biomedical information stored in computerized form. To provide a testing
ground for some of these ideas we have undertaken the development of
SPECIALIST, a prototype system for parsing and accessing biomedical text.
The system includes linguistic and biomedical knowledge. Linguistic
knowledge involves rules and facts about the grammar of the language.
Biomedical knowledge involves rules and facts about the domain of
biomedicine. The UMLS knowledge sources, Meta-1 and the Semantic Network,
as well as the UMLS test collection, have recently contributed to the
development of the SPECIALIST system. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>McCray AT, Aronson AR, Browne AC, Rindflesch TC, Razi A, Srinivasan S.
UMLS knowledge for biomedical language processing. Bull Med Libr Assoc
1993 Apr;81(2):184-94. This paper describes efforts to provide access to
the free text in biomedical databases. The focus of the effort is the
development of SPECIALIST, an experimental natural language processing
system for the biomedical domain. The system includes a broad coverage
parser supported by a large lexicon, modules that provide access to the
extensive Unified Medical Language System (UMLS) Knowledge Sources, and a
retrieval module that permits experiments in information retrieval. The
UMLS Metathesaurus and Semantic Network provide a rich source of
biomedical concepts and their interrelationships. Investigations have been
conducted to determine the type of information required to effect a map
between the language of queries and the language of relevant documents.
Mappings are never straightforward and often involve multiple inferences.
Copyright by and reprinted with permission of the Medical Library
Association.</P>
<P>Murphy SN, Barnett GO. Achieving automated narrative text
interpretation using phrases in the electronic medical record. Proc AMIA
Fall Symp 1996:532-6. Stereotypic phrases are used by clinicians
throughout the medical record, as seen in an analysis of our COSTAR
medical record database. These phrases are often associated with an
underlying semantic concept; for example the phrase CLEAR LUNGS may be
linked with the concept "normal lung exam" for a particular physician.
Formalizing these associations with concepts from the UMLS using the
MEDPhrase application allowed us to automate interpretation of narrative
text within our electronic medical record. Copyright by and reprinted with
permission of the American Medical Informatics Association. </P>
<P>Peng P, Aguirre A, Johnson SB, Cimino JJ. Generating MEDLINE search
strategies using a librarian knowledge-based system. Proc Annu Symp Comput
Appl Med Care 1993:596-600. We describe a librarian knowledge-based system
that generates a search strategy from a query representation based on a
user's information need. Together with the natural language parser AQUA,
the system functions as a human/computer interface, which translates a
user query from free text into a BRS Onsite search formulation, for
searching the MEDLINE bibliographic database. In the system, conceptual
graphs are used to represent the user's information need. The UMLS
Metathesaurus and Semantic Net are used as the key knowledge sources in
building the knowledge base. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Pietrzyk PM. Free text analysis. Int J Biomed Comput 1995
Apr;39(1):139-44. In the context of hospital information systems (HIS)
medical free text analysis is reviewed with respect to current automated
approaches to literature retrieval, case retrieval and fact retrieval from
textual data in the patient record. The Unified Medical Language System
(UMLS) project has enormously stimulated current research. It is expected
that UMLS knowledge sources and SNOMED III (which need a translation into
other languages as soon as possible) as well as the conceptual graphs
formalism, could become standards to utilize free text information
contained in HIS databases.</P>
<P>Sager N, Lyman M, Bucknall C, Nhan N, Tick LJ. Natural language
processing and the representation of clinical data. J Am Med Inform Assoc
1994 Mar-Apr;1(2):142-60. OBJECTIVE: Develop a representation of clinical
observations and actions and a method of processing free-text patient
documents to facilitate applications such as quality assurance. DESIGN:
The Linguistic String Project (LSP) system of New York University utilizes
syntactic analysis, augmented by a sublanguage grammar and an information
structure that are specific to the clinical narrative, to map free-text
documents into a database for querying. MEASUREMENTS: Information
precision (I-P) and information recall (I-R) were measured for queries for
the presence of 13 asthma-health-care quality assurance criteria in a
database generated from 59 discharge letters. RESULTS: I-P, using counts
of major errors only, was 95.7% for the 28-letter training set and 98.6%
for the 31-letter test set. I-R, using counts of major omissions only, was
93.9% for the training set and 92.5% for the test set. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Satomura Y, do Amaral MB. Automated diagnostic indexing by natural
language processing. Med Inf (Lond) 1992 Jul-Sep;17(3):149-63.</P>
<P>Volot F, Zweigenbaum P, Bachimont B, Ben Said M, Bouaud J, Fieschi M,
Boisvieux JF. Structuration and acquisition of medical knowledge. Using
UMLS in the conceptual graph formalism. Proc Annu Symp Comput Appl Med
Care 1993:710-4. The use of a taxonomy, such as the concept type lattice
(CTL) of Conceptual Graphs, is a central structuring piece in a
knowledge-based system. The knowledge it contains is constantly used by
the system, and its structure provides a guide for the acquisition of
other pieces of knowledge. We show how UMLS can be used as a knowledge
resource to build a CTL and how the CTL can help the process of
acquisition for other kinds of knowledge. We illustrate this method in the
context of the MENELAS natural language understanding project. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P><A
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<HR>
<UL>
<LI>
<UL>
<LI><STRONG><A name=3g>Indexing and Retrieval Methods and
Algorithms</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Aronson AR. The effect of textual variation on concept based
information retrieval. Proc AMIA Fall Symp 1996:373-7. Accounting for
textual variation in the documents and queries processed by information
retrieval systems is considered essential for achieving good retrieval.
Recent research has called into question several of the techniques used to
support this endeavor. This paper reports on experiments with a concept
based information retrieval system which relies on a program called
MetaMap to account for textual variation in the process of mapping
biomedical text such as MEDLINE bibliographic citations to the UMLS
Metathesaurus. The experiments confirm that the effort expended in
handling textual variation is well-spent for at least one type of concept
based information retrieval. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P>
<P>Chute CG, Yang Y. An evaluation of concept based latent semantic
indexing for clinical information retrieval. Proc Annu Symp Comput Appl
Med Care 1992:639-43. Latent Semantic Indexing (LSI) of surgical case
report text using ICD-9-CM procedure codes and index terms was evaluated.
The precision-recall performance of this two-step matrix retrieval process
was compared with the SMART Document retrieval system, surface word
matching, and humanly assigned procedure codes. Human coding performed
best, two-step LSI did less well than surface matching or SMART. This
evaluation suggests that concept-based LSI may be compromised by its
two-stage nature and its dependence upon a robust term database linked to
main concepts. However, the potential elegance of partial- credit concept
matching merits the continued evaluation of LSI for clinical case
retrieval. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Chute CG, Yang Y, Evans DA. Latent Semantic Indexing of medical
diagnoses using UMLS semantic structures. Proc Annu Symp Comput Appl Med
Care 1991:185-9. The relational files within the UMLS Metathesaurus
contain rich semantic associations to main concepts. We invoked the
technique of Latent Semantic Indexing to generate information matrices
based on these relationships and created semantic vectors using singular
value decomposition. Evaluations were made on the complete set and subsets
of Metathesaurus main concepts with the semantic type Disease or Syndrome.
Real number matrices were created with main concepts, lexical variants,
synonyms, and associated expressions. Ancestors, children, siblings, and
related terms were added to alternative matrices, preserving the
hierarchical direction of the relation as the imaginary component of a
complex number. Preliminary evaluation suggests that this technique is
robust. A major advantage is the exploitation of semantic features which
derive from a statistical decomposition of UMLS structures, possibly
reducing dependence on the tedious construction of semantic frames by
humans. Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Doszkocs TE, Sass RK. An associative semantic network for machine-aided
indexing, classification and searching. In: Fidel R, Kwasnik BH, Smith PJ,
editors., Proceedings of 3rd ASIS SIG/CR Classification Research Workshop;
1992 Oct 25; Pittsburgh, PA. Medford (NJ): Learned Information; 1993. p.
15-35. Capturing and exploiting textual database associations has played a
pivotal role in the evolution of automated information systems. A variety
of statistical, linguistic and artificial intelligence approaches have
been described in the literature. Many of these R&amp;D concepts and
techniques are now being incorporated into commercially available search
systems and services. This paper discusses prior work and reports on
research in progress aimed at creating and utilizing a global semantic
associative database, AURA (Associative User Retrieval Aid), to facilitate
machine-assisted indexing, classification and searching in the large-scale
information processing environment of NLM's core bibliographic databases,
MEDLINE and CATLINE. AURA is a semantic network of over two million
natural language phrases derived from more than a million MEDLINE titles.
These natural language phrases are associatively linked to NLM's MeSH
(Medical Subject Headings) and UMLS (Unified Medical Language System)
metathesaurus controlled vocabulary and classification resources.
Reproduced with permission of the American Society for Information
Science.</P>
<P>Harbourt AM, Syed EJ, Hole WT, Kingsland LC 3d. The ranking algorithm
of the Coach browser for the UMLS metathesaurus. Proc Annu Symp Comput
Appl Med Care 1993:720-4. This paper presents the novel ranking algorithm
of the Coach Metathesaurus browser which is a major module of the Coach
expert search refinement program. An example shows how the ranking
algorithm can assist in creating a list of candidate terms useful in
augmenting a suboptimal Grateful Med search of MEDLINE. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Hersh WR. Evaluation of Meta-1 for a concept-based approach to the
automated indexing and retrieval of bibliographic and full-text databases.
Med Decis Making 1991 Oct-Dec;11(4 Suppl):S120-4. SAPHIRE is a
concept-based approach to information retrieval in the biomedical domain.
Indexing and retrieval are based on a concept-matching algorithm that
processes free text to identify concepts and map them to their canonical
form. This process requires a large vocabulary containing a breadth of
medical concepts and a diversity of synonym forms, which is provided by
the Meta-1 vocabulary from the Unified Medical Language System Project of
the National Library of Medicine. This paper describes the use of Meta-1
in SAPHIRE and an evaluation of both entities in the context of an
information retrieval study. Copyright 1991 Hanley and Belfus.</P>
<P>Hersh WR, Hickam DH. A comparative analysis of retrieval effectiveness
for three methods of indexing AIDS-related abstracts. In: Proceedings of
the 54th Annual Meeting of the American Society for Information Science;
1991 Oct 27-31; Washington, DC. Medford (NJ): Learned Information; 1991.
p. 211-25. SAPHIRE is an experimental information retrieval system
featuring concept-based automated indexing and natural language input,
relevance-based retrieval. This experiment evaluates SAPHIRE'S indexing
capability in a three-way comparison of retrieval effectiveness versus
traditional MEDLINE indexing and title-abstract word indexing. SAPHIRE's
recall and precision values are inferior to both methods in a
MEDLINE-style Boolean searching environment, although additional
experiments suggest that better retrieval performance is obtained when
SAPHIRE's natural language input and relevance ranking features are
used.</P>
<P>Hersh WR, Hickam DH. A comparison of retrieval effectiveness for three
methods of indexing medical literature. Am J Med Sci 1992
May;303(5):292-300. Conventional approaches to indexing medical literature
include the human assignment of terms from a controlled vocabulary, such
as MeSH, or the computer assignment of all words in the title and abstract
as indexing terms. Human indexing suffers from inconsistency, while
word-based indexing suffers from the multiple meanings of words. SAPHIRE
is a computer program designed to provide indexing using controlled terms
that are assigned by computer, based on their occurrence in the title and
abstract. In this first evaluation of SAPHIRE, the authors compared the
retrieval performance of the three indexing approaches--human-based
MEDLINE with text words; machine-based SAPHIRE with text words; and text
words only--for searches by measuring recall and precision for each search
using a test collection of 200 abstracts. The abstracts were judged by
human reviewers for relevance as applied to 12 literature queries. The
results suggest that text word indexing is more effective than indexing
with MeSH terms. SAPHIRE's indexing performance was slightly inferior but
the program has other advantageous features. Copyright Southern Society
for Clinical Investigation; published by Lippincott-Raven Publishers.</P>
<P>Hersh WR, Hickam DH. A comparison of two methods for indexing and
retrieval from a full-text medical database. Med Decis Making 1993
Jul-Sep;13(3):220-6. The objective of this study was to compare how well
medical professionals are able to retrieve relevant literature references
using two computerized literature searching systems that provide automated
(non-human) indexing of content. The first program was SAPHIRE, which
features concept-based indexing, free-text input of queries, and ranking
of retrieved references for relevance. The second program was SWORD, which
provides single-word searching using Boolean operators (AND, OR). Sixteen
fourth-year medical students participated in the study. The database for
searching was six volumes from the 1989 Yearbook series. The queries were
ten questions generated on teaching rounds. All subjects searched half the
queries with each program. After the searching, each subject was given a
questionnaire about prior experience and preferences about the two
programs . Recall (proportion of relevant articles retrieved from the
database) and precision (proportion of relevant articles in the retrieved
set) were measured for each search done by each participant. Mean recall
was 57.6% with SAPHIRE; it was 58.6% with SWORD. Precision was 48.1% with
SAPHIRE vs 57.6% with SWORD. Each program was rated easier to use than the
other by half of the searchers, and preferences were associated with
better searching performance for that program. Both systems achieved
recall and precision comparable to existing systems and may represent
effective alternatives to MEDLINE and other retrieval systems based on
human indexing for searching medical literature. Copyright 1993 Hanley and
Belfus.</P>
<P>Hersh WR, Hickam DH. An evaluation of interactive boolean and natural
language searching with an online medical textbook. J Am Soc Inf Sci 1995
Aug;46(7):478-89. Few studies have compared the interactive use of Boolean
and natural language searching systems. We studied the use of three
retrieval systems by senior medical students searching on queries
generated by actual physicians in a clinical setting. The searchers were
randomized to search on two of three different retrieval systems: a
Boolean system, a word-based natural language system, and a concept-based
natural language system. Our results showed no statistically significant
differences in recall or precision among the three systems. Likewise, we
found no user preference for any system over the others. In the course of
this study we did find, however, a number of problems with traditional
measures of retrieval evaluation when applied to the interactive search
setting. Copyright 1995 by and reproduced with permission of John Wiley
and Sons. </P>
<P>Hersh WR, Hickam DH, Leone TJ. Words, concepts, or both: optimal
indexing units for automated information retrieval. Proc Annu Symp Comput
Appl Med Care 1992:644-8. What is the best way to represent the content of
documents in an information retrieval system? This study compares the
retrieval effectiveness of five different methods for automated
(machine-assigned) indexing using three test collections. The consistently
best methods are those that use indexing based on the words that occur in
the available text of each document. Methods used to map text into
concepts from a controlled vocabulary showed no advantage over the
word-based methods. This study also looked at an approach to relevance
feedback which showed benefit for both word-based and concept-based
methods. Copyright by and reprinted with permission by the American
Medical Informatics Association.</P>
<P>Jenders RA, Estey G, Martin M, Hamilton G, Ford-Carleton P, Thompson
BT, Oliver DE, Eccles R, Barnett GO, Zielstorff RD, et al. Indexing
guidelines: applications in use of pulmonary artery catheters and pressure
ulcer prevention. Proc Annu Symp Comput Appl Med Care 1994:802-6. In a
busy clinical environment, access to knowledge must be rapid and specific
to the clinical query at hand. This requires indices which support easy
navigation within a knowledge source. We have developed a computer-based
tool for trouble-shooting pulmonary artery waveforms using a graphical
index. Preliminary results of domain knowledge tests for a group of
clinicians exposed to the system (N = 33) show a mean improvement on a
30-point test of 5.33 (p &lt; 0.001) compared to a control group (N = 19)
improvement of 0.47 (p = 0.61). Survey of the experimental group (N = 25)
showed 84% (p = 0.001) found the system easy to use. We discuss lessons
learned in indexing this domain area to computer-based indexing of
guidelines for pressure ulcer prevention. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Merz RB, Cimino C, Barnett GO, Blewett DR, Gnassi JA, Grundmeier R,
Hassan L. A pre-search estimation algorithm for MEDLINE strategies with
qualifiers. Proc Annu Symp Comput Appl Med Care 1994:910-4. Inexperienced
users of online medical databases often have difficulty formulating their
queries. Systems designed to assist them usually do not estimate how
effective the initial search strategy will be before performing an actual
search. Consequently, the search may find an overwhelming number of
citations, or retrieve nothing at all. We have developed an estimation
algorithm to predict the outcome of a MEDLINE search. The portion of the
algorithm described here estimates retrieval for strategies containing
qualifiers. In test searches, the estimate reduced the trial-and-error of
strategy formulation. However, the accuracy of the estimate fell short of
expectations. Our results show that pre-search estimation for strategies
with qualifiers cannot be performed effectively with only the occurrence
data that is presently available. They further imply that automated search
intermediaries can benefit from medical knowledge which expresses the
relationships that exist between terms. Copyright by and reprinted with
permission of the American Medical Informatics Association. </P>
<P>Richwine PW. A study of MeSH and UMLS for subject searching in an
online catalog. Bull Med Libr Assoc 1993 Apr;81(2):229-33.</P>
<P>Rindflesch TC, Aronson AR. Semantic processing in information
retrieval. Proc Annu Symp Comput Appl Med Care 1993:611-5. Intuition
suggests that one way to enhance the information retrieval process would
be the use of phrases to characterize the contents of text. A number of
researchers, however, have noted that phrases alone do not improve
retrieval effectiveness. In this paper we briefly review the use of
phrases in information retrieval and then suggest extensions to this
paradigm using semantic information. We claim that semantic processing,
which can be viewed as expressing relations between the concepts
represented by phrases, will in fact enhance retrieval effectiveness. The
availability of the UMLS domain model, which we exploit extensively,
significantly contributes to the feasibility of this processing. Copyright
by and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Robert JJ, Joubert M, Nal L, Fieschi M. A computational model of
information retrieval with UMLS. Proc Annu Symp Comput Appl Med Care
1994:167-71. A high level representation of data would clarify the complex
collection of medical concepts, terms and relationships derived from
standard classifications that the Unified Medical Language System
contains. A conceptual model is described which represents the data
structure. A second objective of this conceptual model is to provide users
with the capability to build queries to information databases as easily as
possible on the basis of this data structure. The methods used to build
this model are semantic networks and conceptual graphs. The
object-oriented computational model which implements this conceptual model
is detailed. It reuses part of the generic C++ classes of the National
Institutes of Health library. New classes are added to this library to
implement the needed functionalities. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Yang Y, Chute CG. Words or concepts: the features of indexing units and
their optimal use in information retrieval. Proc Annu Symp Comput Appl Med
Care 1993:685-9. Words or Concepts, which are a better choice for indexing
the contents of documents? The answer depends on what method is used for
retrieval. This paper studies the effects of using canonical concepts
versus document words in different retrieval systems with a testing
collection of MEDLINE documents. In our tests, for a retrieval system
which does not use any human knowledge, using words yielded better
retrieval results, while using concepts suffered from a vocabulary
difference between canonical expressions of concepts and non-canonical
words in queries or documents. For a system which depends on the UMLS
synonym set for a mapping from queries or documents to canonical concepts,
the retrieval results were slightly better than the case of not using the
synonyms, but still worse than the systems using words. For the systems
which automatically learn empirical connections between words and concepts
from examples in the testing collection, the vocabulary problem was
effectively solved, and the results of using concepts were competitive or
better, compared to those using words. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P><A
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<HR>
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<UL>
<LI><STRONG><A name=3h>Information Retrieval
Systems</A></STRONG><BR></LI></UL></LI></UL>
<HR>
<P>Hersh W, Hickam D. Information retrieval in medicine: the SAPHIRE
experience. Medinfo 1995;8(Pt 2):1433-7. Information retrieval systems are
proliferating in biomedical settings, but many problems in indexing,
retrieval, and evaluation of systems continue to exist. The SAPHIRE
Project was undertaken to seek solutions to these problems. This paper
summarizes the evaluation studies that have been done with SAPHIRE,
highlighting the lessons learned and laying out the challenges ahead to
all medical information retrieval efforts.</P>
<P>Hersh W, Hickam DH, Haynes RB, McKibbon KA. Evaluation of SAPHIRE: an
automated approach to indexing and retrieving medical literature. Proc
Annu Symp Comput Appl Med Care 1991:808-12. An analysis of SAPHIRE, an
experimental information retrieval system featuring automated indexing and
natural language retrieval, was performed on MEDLINE references using data
previously generated for a MEDLINE evaluation. Compared with searches
performed by novice and expert physicians using MEDLINE, SAPHIRE achieved
comparable recall and precision. While its combined recall and precision
performance did not equal the level of librarians, SAPHIRE did achieve a
significantly higher level of absolute recall. SAPHIRE has other potential
advantages over existing MEDLINE systems. Its natural language interface
does not require knowledge of MeSH, and it provides relevance ranking of
retrieved references. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Hersh W, Leone TJ. The SAPHIRE server: a new algorithm and
implementation. Proc Annu Symp Comput Appl Med Care 1995:858-62. SAPHIRE
is an experimental information retrieval system implemented to test new
approaches to automated indexing and retrieval of medical documents. Due
to limitations in its original concept-matching algorithm, a modified
algorithm has been implemented which allows greater flexibility in partial
matching and different word order within concepts. With the concomitant
growth in client-server applications and the Internet in general, the new
algorithm has been implemented as a server that can be accessed via other
applications on the Internet. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Hersh WR, Greenes RA. SAPHIRE--an information retrieval system
featuring concept matching, automatic indexing, probabilistic retrieval,
and hierarchical relationships. Comput Biomed Res 1990 Oct;23(5):410-25.
SAPHIRE (Semantic and Probabilistic Heuristic Information Retrieval
Environment) is an experimental computer program designed to test new
techniques in automated information retrieval in the biomedical domain. A
main feature of the program is a concept-finding algorithm that processes
free text to find canonical concepts. The algorithm is designed to handle
a wide variety of synonyms and convert them to canonical form. This allows
natural language to be used for query input and also serves as the basis
for a new approach to automatic indexing based on a combination of
probabilistic and linguistic methods. Copyright 1990 Academic Press.</P>
<P>Hersh WR, Hickam D. Information retrieval in medicine. The SAPHIRE
experience. J Am Soc Inf Sci 1995 Dec;46(10):743-7. Information retrieval
systems are being used increasingly in biomedical settings, but many
problems still exist in indexing, retrieval, and evaluation. The SAPHIRE
Project was undertaken to seek solutions for these problems. This article
summarizes the evaluation studies that have been done with SAPHIRE,
highlighting the lessons learned and laying out the challenges ahead to
all medical information retrieval efforts. Copyright 1995 by and
reproduced with permission of John Wiley and Sons.</P>
<P>Hersh WR, Hickam DH, Haynes RB, McKibbon KA. A performance and failure
analysis of SAPHIRE with a MEDLINE test collection. J Am Med Inform Assoc
1994 Jan-Feb;1(1):51-60. OBJECTIVE: Assess the performance of the SAPHIRE
automated information retrieval system. DESIGN: Comparative study of
automated and human searching of a MEDLINE test collection. MEASUREMENTS:
Recall and precision of SAPHIRE were compared with those attributes of
novice physicians, expert physicians, and librarians for a test collection
of 75 queries and 2,334 citations. Failure analysis assessed the efficacy
of the Metathesaurus as a concept vocabulary; the reasons for retrieval of
nonrelevant articles and nonretrieval of relevant articles; and the effect
of changing the weighting formula for relevance ranking of retrieved
articles. RESULTS: Recall and precision of SAPHIRE were comparable to
those of both physician groups, but less than those of librarians.
CONCLUSION: The current version of the Metathesaurus, as utilized by
SAPHIRE, was unable to represent the conceptual content of one-fourth of
physician-generated MEDLINE queries. The most likely cause for retrieval
of nonrelevant articles was the presence of some or all of the search
terms in the article, with frequencies high enough to lead to retrieval.
The most likely cause for nonretrieval of relevant articles was the
absence of the actual terms from the query, with synonyms or
hierarchically related terms present instead. There were significant
variations in performance when SAPHIRE's concept-weighing formulas were
modified. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Hersh WR, Pattison-Gordon E, Evans DA. Adaption of Meta-1 for SAPHIRE,
a general purpose information retrieval system. Proc Annu Symp Comput Appl
Med Care 1990:156-60. The Unified Medical Language Systems Project (UMLS)
of the National Library of Medicine (NLM) has produced Meta-1, a
metathesaurus featuring over 40000 concepts and their synonyms from
several commonly-used medical vocabularies. The authors have adapted
Meta-1 for use in SAPHIRE, an information retrieval system featuring
automated indexing and probabilistic retrieval. They have also built
DESYGNS, a semantic network system designed to contain Meta-1 concepts
along with their sematic relationships. Future plans include improved
concept matching, improved indexing capability, and the use of semantic
relationships. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Jachna JS, Powsner SM, Miller PL. Augmenting GRATEFUL MED with the UMLS
Metathesaurus: an initial evaluation. Bull Med Libr Assoc 1993
Jan;81(1):20-8. Clinicians in patient care settings must be able to locate
relevant recent medical literature quickly. Computer literacy is
increasing, but many clinicians remain ill at ease with search strategies
for online bibliographic databases. As part of an ongoing project to
simplify the translation of clinical questions into effective searches, a
Unified Medical Language System (UMLS) Metathesaurus tool was designed.
The authors compared bibliographic searches by relatively inexperienced
users employing only GRATEFUL MED to searches done using GRATEFUL MED
augmented with this tool. The users were clinicians examining questions
related to a test set of clinical cases. Their problems and successes were
monitored; the results suggest that the addition of a thesaurus helps
resolve some problems in citation retrieval that trouble the novice user.
By helping the user understand indexing terms in context and by reducing
typing errors, a thesaurus can help provide an intelligent solution to
lexical mismatches in bibliographic retrieval. Copyright by and reprinted
with permission of the Medical Library Association.</P>
<P>Joubert M, Riouall D, Fieschi M, Botti G, Proudhon H. Contextual aids
for medical information retrieval. Medinfo 1992;7(Pt 2):1522-7. The paper
presents the first results of a work that the authors began in 1990. This
research work concerns the representation and use of medical concepts in
medical information management. Customisation of the user interfaces and
management of users contexts are addressed. These capabilities enhance the
material furnished by UMLS.</P>
<P>Kingsland LC 3d, Harbourt AM, Syed EJ, Schuyler PL. Coach: applying
UMLS knowledge sources in an expert searcher environment. Bull Med Libr
Assoc 1993 Apr;81(2):178-83. With the development of the Unified Medical
Language System (UMLS) Knowledge Sources, the National Library of Medicine
(NLM) has produced a resource of great potential for improving the
searching of MEDLINE. The Coach expert searcher system, an inhouse
research project at NLM, is designed to help users of the GRATEFUL MED
front-end software improve MEDLINE search and retrieval capabilities. This
paper describes the Coach program, the knowledge sources it uses, and some
of the ways it applies elements of the UMLS Metathesaurus to facilitate
access to the biomedical literature. Copyright by and reprinted with
permission of the Medical Library Association.</P>
<P>Kingsland LC 3d, Syed EJ, Lindberg DA. Coach: an expert searcher
program to assist Grateful Med users searching MEDLINE. Medinfo 1992;7(Pt
1):382-6. The Coach expert searcher system is being developed as an
in-house research project at the USA National Library of Medicine (NLM).
It brings to bear the Unified Medical Language System (UMLS) Metathesaurus
and ten additional knowledge sources to assist Grateful Med users seeking
help in improving retrieval from the ELHILL mainframe retrieval engine.
Initial work has concentrated on MEDLINE and its backfiles, and in
particular on the problem of null retrieval. Subsequent functions will
address searching problems relevant to other MEDLARS files. Coach offers
true ELHILL multifile searches, ELHILL sorting of output citations before
download, and considerable flexibility in the print format of downloaded
results. It works interactively with the user, with Grateful Med and with
ELHILL.</P><A
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<HR>
<UL>
<LI><STRONG><A name=3i>Linking Clinical Systems to Knowledge-based
Information Sources</A></STRONG><BR></LI></UL>
<HR>
<P>Cimino JJ. Linking patient information systems to bibliographic
resources. Methods Inf Med 1996 Jun;35(2):122-6. Medical informatics
researchers have explored a number of ways to integrate medical
information resources into patient care systems. Particular attention has
been given to the integration of on-line bibliographic resources. This
paper presents an information model which breaks down the integration task
into three components, each of which answers a question: what is the
user's question?, where can the answer be found?, and how is the retrieval
strategy composed? Twelve experimental systems are reviewed and their
methods for addressing one or more of these questions are described. </P>
<P>Cimino JJ, Aguirre A, Johnson SB, Peng P. Generic queries for meeting
clinical information needs. Bull Med Libr Assoc 1993 Apr;81(2):195-206.
This paper describes a model for automated information retrieval in which
questions posed by clinical users are analyzed to establish common
syntactic and semantic patterns. The patterns are used to develop a set of
general-purpose questions called generic queries. These generic queries
are used in responding to specific clinical information needs. Users
select generic queries in one of two ways. The user may type in questions,
which are then analyzed, using natural language processing techniques, to
identify the most relevant generic query; or the user may indicate patient
data of interest and then pick one of several potentially relevant
questions. Once the query and medical concepts have been determined, an
information source is selected automatically, a retrieval strategy is
composed and executed, and the results are sorted and filtered for
presentation to the user. This work makes extensive use of the National
Library of Medicine's Unified Medical Language System (UMLS): medical
concepts are derived from the Metathesaurus, medical queries are based on
semantic relations drawn from the UMLS Semantic Network, and automated
source selection makes use of the Information Sources Map. The paper
describes research currently under way to implement this model and reports
on experience and results to date. Copyright by and reprinted with
permission of the Medical Library Association.</P>
<P>Cimino JJ, Johnson SB, Aguirre A, Roderer N, Clayton PD. The MEDLINE
Button. Proc Annu Symp Comput Appl Med Care 1992:81-5. We have developed a
computerized method for performing bibliographic searches directly from
patient data involving five steps: 1) identifying specific patient data
which raises a question in the mind of the user, 2) selection (from a list
of generic questions) of a small number of questions which fit the
selected patient data, 3) automated translation of the patient data into
appropriate terms used for bibliographic indexing, 4) conversion of the
question selected by the user into a search strategy, and 5) transfer of
the search strategy to a search engine for a bibliographic database. We
have modified the Columbia-Presbyterian Clinical Information System to
experiment with this method. The first implementation converts patient
diagnoses and procedures coded in ICD9-CM into Medical Subject Headings
(MeSH) and searches Medline using BRS/Onsite. Challenges include
development of a useful set of generic questions and translation from
ICD9-CM to MeSH using the Unified Medical Language System (UMLS).
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Cimino JJ, Johnson SB, Peng P, Aguirre A. From ICD9-CM to MeSH using
the UMLS: a how-to guide. Proc Annu Symp Comput Appl Med Care 1993:730-4.
One purpose of the Unified Medical Language System (UMLS) is to facilitate
conversion of terms from one controlled medical vocabulary to another. We
examined our ability to convert International Classification of Diseases,
9th Edition, Clinical Modifications (ICD9-CM) to Medical Subject Headings
(MeSH) using the UMLS. We describe a method which mapped 30.4% of ICD9-CM
to UMLS. Of these, 95.0% were linked to MeSH, of which translation was
straightforward in 90.4%. We discuss the use of these translations for
retrieval from MeSH-indexed databases, such as Medline. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Cimino JJ, Sideli RV. Using the UMLS to bring the library to the
bedside. Med Decis Making 1991 Oct-Dec;11(4 Suppl):S116-20. This paper
presents an algorithm that can be used to convert ICD9 terms to related
MeSH terms. Preliminary evaluation indicates that together, the algorithm
and the UMLS provide a reasonable resource for facilitating such
conversions. Copyright 1991 Hanley and Belfus.</P>
<P>Lowe HJ, Walker WK, Polonkey Se, Jiang F, Vries JK, McCray AT. The
image engine HPCC project: a medical digital library system using
agent-based technology to create an integrated view of the electronic
medical record. In: Adam N, Halem M, Yesha Y, editors. Proceedings of the
3rd Forum on Research and Technology Advances in Digital Libraries, ADL
'96. Los Alamitos: IEEE Computer Society Press; 1996. p. 45-56.</P>
<P>Merz RB, Cimino C, Barnett GO, Blewett DR, Gnassi JA, Grundmeier R,
Hassan L. Q &amp; A: a query formulation assistant. Proc Annu Symp Comput
Appl Med Care 1993:498-502. Inexperienced users of online medical
databases often do not know how to formulate their queries for effective
searches. Previous attempts to help them have provided some standard
procedures for query formulation, but depend on the user to enter the
concepts of a query properly so that the correct search strategy will be
formed. Intelligent assistance specific to a particular query often is not
given. Several systems do refine the initial strategy based on relevance
feedback but usually do not make an effort to determine how well-formed a
query is before actually performing the search. As part of the Interactive
Query Workstation (IQW), we have developed an expert system, Questions and
Answers (Q&amp;A), that assists in formulating an initial strategy given
concepts entered by the user and that determines if the strategy is
well-formed, refining it when necessary. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Miller PL, Frawley SJ. Trade-offs in producing patient-specific
recommendations from a computer-based clinical guideline: a case study. J
Am Med Inform Assoc 1995 Jul-Aug;2(4):238-42. This case study explored 1)
how much online clinical data is required to obtain patient-specific
recommendations from a computer-based clinical practice guideline, 2)
whether the availability of increasing amounts of online clinical data
might allow a higher specificity of those recommendations, and 3) whether
that increased specificity is necessarily desirable. The "quick reference
guide" version of the guideline for acute postoperative pain management in
adults, developed by the Agency for Health Care Policy and Research, was
analyzed. Patient-specific data items that might be used to tailor the
computer's output for a particular case were grouped into rough categories
depending on how likely they were to be available online and how readily
they might be determined from online clinical data. The patient-specific
recommendations were analyzed to determine to what degree the amount of
text produced depended on the online availability of different categories
of data. An examination of example recommendations, however, illustrated
that high specificity may not always be desirable. The study provides a
concrete illustration of how the richness of online clinical data can
affect patient-specific recommendations, and describes a number of related
design trade-offs in converting a clinical guideline into an interactive,
computer-based form. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Miller RA, Gieszczykiewicz FM, Vries JK, Cooper GF. CHARTLINE:
providing bibliographic references relevant to patient charts using the
UMLS Metathesaurus Knowledge Sources. Proc Annu Symp Comput Appl Med Care
1992:86-90. A successful medical informatics program helps its users to
match their information needs as closely and efficiently as possible to
the capabilities of the system. CHARTLINE is a computer program whose
input is a free text, natural language patient chart in ASCII format.
Using the UMLS Metathesaurus Knowledge Sources, CHARTLINE can suggest
bibliographic references relevant to the patient case described in the
chart. The program does not attempt to understand the natural language
content of the chart. CHARTLINE only recognizes UMLS Metathesaurus Main
Concept terms (or their synonyms) as they occur in the medical text, since
those terms represent the tokens used to index the literature. The program
depends on user feedback to determine which topics of a large number of
potentially relevant subjects are of interest to the user. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Nelson SJ, Sherertz DD, Tuttle MS. Issues in the development of an
information retrieval system: the Physician's Information Assistant.
Medinfo 1992;7(Pt 1):371-5. There are many models of electronic
information retrieval systems. The diversity of these systems, each
requiring the user to learn new and idiosyncratic operating methods, is
inhibiting to the user. In an effort to find a useful set of conventions
of information organization and user navigation, the authors have
developed the Physician's Information System (PIA). The model is that of a
hypertext browser which reflects an assessment of the manner a user is
most likely to approach the knowledge (the user model). The PIA uses
existing knowledge bases and resources, including a semantic network
browser and a communications program which handles literature searches,
and achieves interoperability over these multiple resources. Browsing
allows a wide variety of cognitive styles and supports answering
poorly-formed queries. The user must exercise judgment in determining if
the information found is relevant to the clinical situation. Difficulties
with large volumes of text on a CRT screen can occur; nontextual visual
representations of information, such as maps, appear to be helpful in
reducing the amount of text. The methodology used in building the PIA
appears to be adaptable to a variety of knowledge sources and other
resources. The consistent user metaphor provides an example of the type of
conventions that may be necessary to enable users to approach multiple
knowledge sources.</P>
<P>Nelson SJ, Sherertz DD, Tuttle MS, Abarbanel RA, Olson NE, Erlbaum MS,
Sperzel WD. The Physician's Information Assistant. Proc Annu Symp Comput
Appl Med Care 1991:950-2.</P>
<P>Patil RS, Silva JS, Swartout WR. An architecture for a health care
provider's workstation. Int J Biomed Comput 1994 Jan;34(1-4):285-99. This
paper presents an architecture for a health care provider's workstation
designed to assist health care providers in performing their daily
activities. The design is based on the concept of a clinician's associate
which acts as an intelligent intermediary between the provider and a
diverse collection of clinical, administrative, and educational
information sources. The architecture is designed to be hardware platform
independent, to work across different I/O capabilities, and to be open,
allowing specialized applications to be easily integrated with the system
and their functionality delivered through a common user environment.</P>
<P>Powsner SM, Miller PL. Automated online transition from the medical
record to the psychiatric literature. Methods Inf Med 1992
Sep;31(3):169-74. Psych Topix is a knowledge-based program which guides
the clinician from an on-line clinical report to a search of the
psychiatric literature or of other relevant databases. It provides this
guidance by using an outline of key topics in a clinical field to provide
"concept-based" links. Each topic is augmented with an activation
expression to signal when that topic is potentially relevant to a case,
and with database search expressions to allow focused retrieval of
information. The bibliographic retrieval component of Psych Topix is
currently operational as part of the daily, routine operation of a
psychiatric consultation service. The system is also implemented in a
demonstration mode to provide retrieval from three additional textual
databases. The current Psych Topix system provides a working demonstration
of the clinical feasibility of using concept-based links to facilitate the
focused, automated transition between on-line medical databases.</P>
<P>Powsner SM, Miller PL. From patient reports to bibliographic retrieval:
a Meta-1 front-end. Proc Annu Symp Comput Appl Med Care 1991:526-30. A
software front-end has been programmed to help construct Medline query
expressions from selected text in clinical records. The user clicks to
choose pertinent words or phrases from the text with a pointing device and
the words are translated into Medical Subject Headings (MeSH). The
National Library of Medicine's Unified Medical Language System Meta-1
Thesaurus is used to look up the words selected by the user. The software
traces through chains of synonyms to assemble a small set of MeSH indexing
terms. The user then makes the final selection from among the MeSH terms
and combines chosen terms using logical connectives to form a Medline
query which is passed on to Grateful Med. This approach provides the
clinical user with a natural starting point, the text of a patient report
with no need to know the MeSH terminology. The software handles the
translation that otherwise would necessitate looking up terms in MeSH
guidebooks, as well as handling the added drudgery of checking out
different synonyms. Preliminary evaluation of this approach with clinical
trainees indicated that they find the front-end a straightforward way to
search for literature relevant to a clinical case. Having a tool for
immediate translation from clinical terminology to indexing terminology
seems to be an important factor. Apparently minor issues in interface
design, such as keeping the clinical report displayed simultaneously along
with the search under construction, and keeping both visible during the
search itself seem to help orient the user. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Powsner SM, Miller PL. Linking bibliographic retrieval to clinical
reports. PsychTopix. Proc Annu Symp Comput Appl Med Care 1989:431-5.
PsychTopix is an expert system which guides the clinician from a computer
based clinical record to a focused bibliographic retrieval. Specifically,
PsychTopix searches the literature for references pertinent to a
psychiatric consultation report. It provides intelligent guidance by
drawing on a knowledge base of current issues in psychiatry. It scans the
report to determine which clinical topics (issues) are likely to be
relevant to the case. The clinician then selects those topics for which he
or she desires a literature search. There is no need for the user to know
the mechanics or protocols of computerized literature retrieval.
PsychTopix initiates a Medline search and presents the references
retrieved to the user. More generally, PsychTopix provides an effective
demonstration of the key topics approach to medical database linkage.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Powsner SM, Riely CA, Barwick KW, Morrow JS, Miller PL. Automated
bibliographic retrieval based on current topics in hepatology: Hepatopix.
Comput Biomed Res 1989 Dec;22(6):552-64. The Hepatopix computer program
helps the physician go from a computerized clinical record directly to a
computerized search of the medical literature. The program uses a
hierarchical list of current (key) topics in hepatology to offer
"intelligent" searches. Each topic has associated "selection logic" and a
tested Medline search. Starting with a liver biopsy case record, Hepatopix
evaluates the selection logic to determine which topics may be pertinent
to the case (based on clinical findings, lab tests, and critical words or
phrases in the summary). The physician then picks those topics which are
interesting enough to warrant a literature search. The citations are
retrieved using search strategies stored for each topic and presented.
Hepatopix is operational with over 200 topics in the realm of liver
neoplasms, operating on liver biopsy case summaries from the Klatskin
Database of Liver Biopsies. Besides demonstrating clinical case-directed
bibliographic retrieval, it demonstrates the utility of a "key topics"
list as a bridge between medical databases. Copyright 1989 Academic
Press.</P>
<P>Sherertz DD, Tuttle MS, Olson NE, Hsu GT, Carlson RW, Fagan LM, Acuff
RD, Cole WG, Nelson SJ. Accessing oncology information at the point of
care: experience using speech, pen, and 3-D interfaces with a knowledge
server. Medinfo 1995;8(Pt 1):792-5. Oncologists' information needs arise
at diverse times and settings. For example: Is superior vena cava syndrome
a medical emergency? Our collaborative group is developing a system that
supports an interface with combinations of spoken, gestural, and simulated
three-dimensional manipulation to help an oncologist focus on the
information need, not the system. The system requires a small amount of
input from the oncologist, and then anticipates what information is
pertinent to the patient at hand, based on the sources it has available.
The system makes use of a Knowledge Server to find relevant information.
The Knowledge Server uses selected data for the particular patient from a
Computer-based Patient Record (CPR) to provide context for the information
needs. The Knowledge Server leverages the Unified Medical Language System
(UMLS) resources as well as relevant communications standards. A layered,
interaction protocol is used to help manage the fulfillment of information
needs. Each of the oncology knowledge sources is transformed into a
uniform representation that utilizes both its formal schema (e.g., its
table of contents) and its concepts and words indexed through the UMLS
Metathesaurus. Our focus on the appropriate use of information from a CPR,
and on anticipating oncologists' information needs, resulted from our
study of several longitudinal patient scenarios. We believe that our use
of scenario-based design techniques will help to ensure the system's
success.</P>
<P>Tuttle MS, Sherertz DD, Fagan LM, Carlson RW, Cole WG, Schipma PB,
Nelson SJ. Toward an interim standard for patient-centered
knowledge-access. Proc Annu Symp Comput Appl Med Care 1993:564-8. Most
care-giver knowledge needs arise at the point of care and are
patient-centered. Many of these knowledge needs can be met using existing
on-line knowledge sources, but the process is too time-consuming,
currently, for even the computer-proficient. We are developing a set of
public domain standards aimed at bringing potentially relevant knowledge
to the point of care in a straight-forward and timely fashion. The
standards will a) make use of selected items from a Computer-based Patient
Record (CPR), e.g., a diagnosis and measure of severity, b) anticipate
certain care-giver knowledge needs, e.g., therapy, protocols,
complications, and c) try to satisfy those needs from available knowledge
sources, e.g., knowledge-bases, citation databases, practice guidelines,
and on-line textbooks. The standards will use templates, i.e.,
fill-in-the-blank structures, to anticipate knowledge needs and UMLS
Metathesaurus enhancements to represent the content of knowledge sources.
Together, the standards will form the specification for a Knowledge-Server
(KS) designed to be accessed from any CPR system. Plans are in place to
test an interim version of this specification in the context of medical
oncology. We are accumulating anecdotal evidence that a KS operating in
conjunction with a CPR is much more compelling to users than either a CPR
or a KS operating alone. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Tuttle MS, Sherertz DD, Olson NE, Nelson SJ, Erlbaum MS, Keck KD, Davis
AN, Suarez-Munist ON, Lipow SS, Cole WG. Toward reusable software
components at the point of care. Proc AMIA Fall Symp 1996:150-4. An
architecture built from five software components -- a Router, Parser,
Matcher, Mapper, and Server -- fulfills key requirements common to several
point-of-care information and knowledge processing tasks. The requirements
include problem-list creation, exploiting the contents of the Electronic
Medical Record for the patient at hand, knowledge access, and support for
semantic visualization and software agents. The components use the
National Library of Medicine Unified Medical Language System to create and
exploit lexical closure -- a state in which terms, text and reference
models are represented explicitly and consistently. Preliminary versions
of the components are in use in an oncology knowledge server. Copyright by
and reprinted with permission of the American Medical Informatics
Association. </P>
<P>van Mulligen EM. UMLS-based access to CPR data. Proc AMIA Fall Symp
1996:819. This abstract describes the results of a project that explores
the use the Unified Medical Language System (UMLS) in browsing a
computer-based patient record (CPR)]. The project consisted of a number of
steps: the mapping between CPR terms and UMLS concepts, the development of
an algorithm that explores the CPR data using this mapping, and the
implementation of a first prototype browser that visualizes "found" data.
A second issue in this project has been the direct access to online
medical literature (MEDLINE) using the UMLS concepts found in the CPR
data. In this project, we used a preliminary version of the Open Records
for Patient Care (ORCA) CPR that consisted only of the history and
physical examination data of patients suffering from heart failure.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=3j>Access to Multiple Knowledge-based Information
Sources</A></STRONG><BR></LI></UL>
<HR>
<P>Barber S, Fowler J, Long KB, Dargahi R, Meyer B. Integrating the UMLS
into VNS retriever. Proc Annu Symp Comput Appl Med Care 1992:273-7. We are
developing a networked resource for the National Library of Medicine's
Unified Medical Language System. We call this resource the UMLS Retriever,
which is an instance of our VNS Retriever architecture. Our prototype user
interface makes use of the Virtual Notebook System Browser. The
development of a networked UMLS service will result in numerous advantages
to our user community. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Cimino C, Barnett GO. Standardizing access to computer-based medical
resources. Proc Annu Symp Comput Appl Med Care 1990:33-7. The paper
describes a working Interactive Query Workstation (IQW). The IQW allows
users to query multiple resources: a medical knowledge base (DXplain), a
clinical database (COSTAR/MQL), a bibliographic database (MEDLINE), a
cancer database (PDQ), and a drug interaction database (PDR). The IQW has
evolved from requiring alteration of resource code to using off-the-shelf
products (Kappa &amp; Microsoft Windows) to control resources.
Descriptions of each resource were developed to allow IQW to access these
resources. There are three components to these descriptions; information
on how data is sent and received from a resource, in formation on types of
queries to which a resource can respond, and information on what types of
information are needed to execute a query. These components form the basis
of a standard description of resources. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Cimino C, Barnett GO, Blewett DR, Hassan LJ, Grundmeier R, Merz R, Kahn
JA, Gnassi JA. Interactive query workstation: a demonstration of the
practical use of UMLS knowledge sources. Proc Annu Symp Comput Appl Med
Care 1992:823-4. The Interactive Query Workstation (IQW) has been
developed to provide clinicians with a uniform program interface for
retrieving medical-related information from various computer-based
information resources. These resources can vary in content (bibliographic
databases, drug information, general medical text databases), function
(article retrieval, differential diagnosis, drug interaction detection, or
drug dosage and administration information), and media formats (local hard
disk, CD-ROM, local area network, or distant telecommunication link). IQW
allows modular addition of new resources as well as extension of
previously installed resources. The National Library of Medicine's three
Unified Medical Language System (UMLS) Knowledge Sources, the
Metathesaurus (Meta), the Semantic Network, and the Information Sources
Map (ISM) have been incorporated into many aspects of IQW. Meta provides
information about medical terminology and aids IQW in isolating the basic
concepts from a clinician's question. The Semantic Network provides
information about the categorization of concepts and possible relations
between concepts. It also assists IQW in determining which queries are
appropriate for a set of concepts contained in the clinician's question.
The ISM provides information about the content available from a
computer-based resources and aids IQW in selecting an appropriate resource
from which to collect information. The computer-based resource selection
is performed without user intervention. This interactive demonstration
shows an environment which increases the accessibility of medical
information to clinicians by utilizing the three UMLS Knowledge Sources.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Cimino C, Barnett GO, Hassan L, Blewett DR, Piggins JL. Interactive
query workstation: standardizing access to computer-based medical
resources. Comput Methods Programs Biomed 1991 Aug;35(4):293-9. Methods of
using multiple computer-based medical resources efficiently have
previously required either the user to manage the choice of resource and
terms, or specialized programming. Standardized descriptions of what
resources can do and how they may be accessed would allow the creation of
an interface for multiple resources. This interface would assist a user in
formulating queries, accessing the resources and managing the results.
This paper describes a working prototype, the Interactive Query
Workstation (IQW). The IQW allows users to query multiple resources: a
medical knowledge base (DXplain), a clinical database (COSTAR/MQL), a
bibliographic database (MEDLINE), a cancer database (PDQ), and a drug
interaction database (PDR). Descriptions of each resource were developed
to allow IQW to access these resources. The descriptions are composed of
information on how data are sent and received from a resource, information
on types of query to which a resource can respond, and information on what
types of information are needed to execute a query. These components form
the basis of a standard description of resources.</P>
<P>Clyman JI, Powsner SM, Paton JA, Miller PL. Using a network menu and
the UMLS Information Sources Map to facilitate access to online reference
materials. Bull Med Libr Assoc 1993 Apr;81(2):207-16. As computer
technology advances, clinicians and biomedical researchers are becoming
more dependent upon information from online databases and information
systems. By using specially configured computer workstations and
high-speed computer networks, it is now possible to access this
information in a rapid and straightforward manner. To empower users by
providing these capabilities, the authors are assembling a variety of
network workstations to be located throughout Yale-New Haven Medical
Center. At the heart of the workstation is NetMenu, a program designed to
help users connect to a number of important online information systems,
including a hospital order entry and results reporting system, a drug
reference, bibliographic retrieval systems, and educational programs. In
addition, as part of the National Library of Medicine's Unified Medical
Language System (UMLS) project, the authors have developed a local
prototype of the UMLS Information Sources Map (ISM) and a companion query
assistant program to complement the NetMenu in helping users select and
connect automatically to information services relevant to a particular
question. The ISM query assistant draws from a listing of many online
information sources accessible via local and international networks.
Copyright by and reprinted with permission of the Medical Library
Association.</P>
<P>Dolin RH. Internet medical resources [letter]. Ann Intern Med 1996 Feb
1;124(3):375. Comment on: Ann Intern Med 1995 Jul 15;123(2):123-31.</P>
<P>Freiburger G, Levy SR, LePoer PM, Murray J, Heinold S, Warfield T. UMLS
workstation project. Progress to date. Proc Annu Symp Comput Appl Med Care
1993:877. In 1992, the Health Science Library at the University of
Maryland was awarded a three-year grant from the National Library of
Medicine to create a Windows-based interface to the Unified Medical
Language System (UMLS). This interface will use the UMLS Knowledge Sources
to assist users searching various databases available at the Library,
including the online catalog, PsycLIT, CINAHL, MEDLINE, and HSL Current
Contents. This paper traces the evolution of the interface during its
first 18 months by illustrating the revisions made to the prototype.
Revisions are based on user feedback elicited in an iterative process of
design, development, and review. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Gnassi JA, Barnett GO. A survey of electronic drug information
resources and identification of problems associated with the differing
vocabularies used to key them. Proc Annu Symp Comput Appl Med Care
1994:631-5. Drug information resources are increasingly becoming
electronically available. They differ in scope, granularity, and purpose.
These considerations have shaped the selection of dissimilar drug name
keys, complicating access. An abbreviated and simplified historical
context of the development of official controlled vocabularies and their
relationships is followed by a review of the kinds of information
available in several electronic drug information resources. The key
vocabularies used are discussed with examples. Problems using the
differing terms of the resource vocabularies are identified. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Gnassi JA, Bormel JI, Blewett DR, Kim RJ, Barnett GO. A medical
information resource server: one stop shopping on the Internet. Proc Annu
Symp Comput Appl Med Care 1994:1025.</P>
<P>Hersh WR, Brown KE, Donohoe LC, Campbell EM, Horacek AE. CliniWeb:
managing clinical information on the World Wide Web. J Am Med Inform Assoc
1996 Jul-Aug;3(4):273-80. The World Wide Web is a powerful new way to
deliver on-line clinical information, but several problems limit its value
to health care professionals: content is highly distributed and difficult
to find, clinical information is not separated from non-clinical
information, and the current Web technology is unable to support some
advanced retrieval capabilities. A system called CliniWeb has been
developed to address these problems. CliniWeb is an index to clinical
information on the World Wide Web, providing a browsing and searching
interface to clinical content at the level of the health care student or
provider. Its database contains a list of clinical information resources
on the Web that are indexed by terms from the Medical Subject Headings
disease tree and retrieved with the assistance of SAPHIRE. Limitations of
the processes used to build the database are discussed, together with
directions for future research. Copyright by and reprinted with permission
of the American Medical Informatics Association.</P>
<P>Loonsk JW, Lively R, TinHan E, Litt H. Implementing the Medical
Desktop: tools for the integration of independent information resources.
Proc Annu Symp Comput Appl Med Care 1991:574-7. The increasing
availability of medical information resources has moved the Medical
Desktop from a theoretical construct to a practical necessity. Many
micro-computers are becoming available in clinical and academic settings
that can access several medical information applications. These computers
are usually not powerful workstations that are part of a clinically
oriented information support system, but are personal computers with
varied capabilities. The applications on these computers come from
different sources, are accessed through different user interfaces and do
not share data well. The de facto Medical Desktop this situation presents
will discourage most end-users because the combination of applications is
complex, the applications are poorly integrated, and individual
applications are inconsistent. At the State University of New York at
Buffalo School of Medicine and Biomedical Sciences we have developed
several Microsoft Windows-based tools that accept a systems level
diversity of resources, but work toward the construction of a coherent
Medical Desktop. These tools include a lexical term linker, a resource
database, and a context sensitive help system that is tailored to locally
available resources. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Rodgers RP. Automated retrieval from multiple disparate information
sources. The World Wide Web and the NLM's Sourcerer project. J Am Soc Inf
Sci 1995 Dec;46(10):755-64. The burgeoning amount of information available
via the internet has heightened awareness of the need for improved tools
for resource identification. The U.S. National Library of Medicine's (NLM)
Sourcerer project is developing software which accepts a user query,
automatically identifies appropriate information resources, and
facilitates connection to those sources for information retrieval. The
current Sourcerer prototype utilizes the
multimedia/multiplatform/multiprotocol network-based hypertext system
known as World Wide Web. It also relies upon the knowledge sources of the
Unified Medical Language System (UMLS). The UMLS is the result of a
long-term project of NLM. It comprises a large Metathesaurus of biomedical
concepts (coupled with a semantic network and syntactical/lexical software
tools) and the information Sources Map (ISM), a database of records
describing specific biomedical information resources. Recent advances in
the standardization of information exchange over computer networks,
coupled with the tools provided by UMLS, facilitate query refinement and
augmentation, connection to resources, and retrieval from resources.
Daunting challenges remain with respect to optimizing resource
descriptions, defining optimal algorithms for searching for sources,
optimizing user interface design, and organizing retrieved information.
Copyright 1995 by and reproduced with permission of John Wiley and
Sons.</P>
<P>Sperzel WD, Abarbanel RM, Nelson SJ, Erlbaum MS, Sherertz DD, Tuttle
MS, Olson NE, Fuller LF. Biomedical database inter-connectivity: an
experiment linking MIM, GENBANK, and META-1 via MEDLINE. Proc Annu Symp
Comput Appl Med Care 1991:190-3. The linkage of disparate biomedical
databases is an important goal of the Unified Medical Language (UMLS)
Project. We conducted an experiment to investigate the feasibility of
using UMLS resources to link databases in clinical genetics and molecular
biology. References from MIM (Mendelian Inheritance in Man) were lexically
mapped to the equivalent citations in MEDLINE. The MeSH major subject
headings by which the citations in a particular MIM entry had been indexed
were used to develop a genetic-disorder-centered view of the world in
Meta-1 (the first official version of the UMLS Metathesaurus). Our
hypothesis was that these MeSH subject headings could provide access to a
semantic neighborhood in Meta-1 that would be relevant to a particular
genetic disorder. By browsing in this semantic neighborhood, a user could
select various combinations of terms with which to search MEDLINE through
an interface between Meta-1 and Grateful Med. Such searches might retrieve
citations that were more recent than those in MIM or that provided useful
supplementary information. Since some MEDLINE records contain pointers to
entries in GENBANK, information about genetic sequences related to a
particular clinical genetic disorder could also be retrieved. This
scenario was implemented for a small number of MIM entries, providing a
concrete demonstration that linking disparate electronic databases in an
important subdomain of biomedicine is relatively straightforward.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Tuttle MS, Cole WG, Sherertz DD, Nelson SJ. Navigating to knowledge.
Methods Inf Med 1995 Mar;34(1-2):214-31. One way to fulfill point-of-care
knowledge needs is to present caregivers with a visual representation of
the available "answers". Using such a representation, caregivers can
recognize what they want, rather than have to recall what they need, and
then navigate to an appropriate answer. Given selected pieces of
information from a computer-based patient record, an interface can
anticipate certain knowledge needs by initializing caregiver navigation in
a semantic neighbourhood on answers likely to be relevant to the patient a
hand. These notions draw heavily on two collaborative projects - the U.S.
National Library of Medicine Unified Medical Language System and the U.S.
National Cancer Institute Knowledge Server. Both these projects support
navigation because they make the structure of medical knowledge explicit
in a way that can be exploited by human interfaces.</P><A
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<HR>
<H3>Preliminary and Ancillary Studies</H3>
<UL>
<LI><STRONG><A name=4a>User Information Needs</A></STRONG> </LI></UL>
<HR>
<P>Cimino C, Barnett GO. Analysis of physician questions in an ambulatory
care setting. Proc Annu Symp Comput Appl Med Care 1991:995-9. We collected
38 questions generated by physicians based on their active patient medical
records. Each question was associated with a single term in a specific
record (Key Term). These questions were analyzed with respect to word
content and concept content. Concepts were matched to the National Library
of Medicine's Metathesaurus (Meta-1). Thirty-seven Key Terms matched
completely to Meta-1 terms. Each question matched to an average of 4.1
Meta-1 terms for a total of 156 concepts. Based on word count, these 156
concepts accounted for 40 percent, stop words accounted for 39 percent,
and numbers and drug trade names accounted for less than 1 percent of the
words. The remaining 20 percent of the words could be matched to 69
concepts not in Meta-1. Review of all concepts showed that they could be
divided into medical terms (Noun Concepts), modifiers (Modifier Concepts),
and concepts that provided context for the questions (Relation Concepts).
The majority of Relation Concepts did not match to Meta-1. A vocabulary of
Relation Concepts would provide a useful starting point for a computer
system designed to aid physicians in answering clinical questions.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Cimino C, Barnett GO. Analysis of physician questions in an ambulatory
care setting. Comput Biomed Res 1992 Aug;25(4):366-73. We collected 69
questions generated by physicians based on their active patient medical
records. Each question was associated with a single term in a specific
record (Key Term). These questions were analyzed with respect to word
content and concept content. Concepts were matched to the National Library
of Medicine's Metathesaurus (Meta-1). Sixty-eight Key Terms were
completely matched by Meta-1 terms. Each question matched to an average of
3.7 Meta-1 terms for a total of 255 concepts. Based on word count, these
255 concepts accounted for 43%, stop words accounted for 36%, and numbers
and drug trade names accounted for 3% of the words. The remaining 18% of
the words could be matched to 143 concepts not in Meta-1. Review of all
concepts showed that they could be divided into medical terms (Noun
Concepts), modifiers (Modifier Concepts), and concepts that provided
context for the questions (Relation Concepts). The majority of Relation
Concepts did not match concepts in Meta-1. A vocabulary of Relation
Concepts would provide a useful starting point for a computer system
designed to aid physicians in answering these questions. Copyright 1992
Academic Press.</P>
<P>Forsythe DE, Buchanan BG, Osheroff JA, Miller RA. Expanding the concept
of medical information: an observational study of physicians' information
needs. Comput Biomed Res 1992 Apr;25(2):181-200. The authors describe an
empirical study of information needs in four clinical settings in internal
medicine in a university teaching hospital. In contrast to the
retrospective data often used in previous studies, this research used
ethnographic techniques to facilitate direct observation of communication
about information needs. On the basis of this experience, the authors
address two main issues: how to identify and interpret expressions of
information needs in medicine and how to broaden ones conception of
'information needs' to account for the empirical data. Copyright 1992
Academic Press.</P>
<P>Osheroff JA, Forsythe DE, Buchanan BG, Bankowitz RA, Blumenfeld BH,
Miller RA. Physicians' information needs: analysis of questions posed
during clinical teaching. Ann Intern Med 1991 Apr 1;114(7):576-81.
OBJECTIVE: To describe information requests expressed during clinical
teaching. SETTING: Residents' work rounds, attending rounds, morning
report, and interns' clinic in a university-based general medicine
service. SUBJECTS: Attending physicians, medical house staff, and medical
students in a general medicine training program. METHODS: An
anthropologist observed communication among study subjects and recorded in
field notes expressions of a need for information. We developed a coding
scheme for describing information requests and applied the coding scheme
to the data recorded. Based on assigned codes, we created a subset of
strictly clinical requests. MEASUREMENTS: Five hundred nineteen
information requests recorded during 17 hours of observed clinical
activity were selected for detailed analysis. These requests related to
the care of approximately 90 patients by 24 physicians and medical
students. Sixty-five requests were excluded because they were not strictly
clinical, leaving a subset of 454 clinical questions for analysis. MAIN
RESULTS: On average, five clinical questions were raised for each patient
discussed. Three hundred thirty-seven requests (74%) concerned patient
care. Of these 337 questions, 175 (52%) requested a fact that could have
been found in a medical record. Seventy-seven (23%) of these questions,
motivated by the needs of patient care, were potentially answerable by a
library, a textbook, a journal, or MEDLINE. Eighty-eight (26%) of the
questions asked for patient care required synthesis of patient information
and medical knowledge. CONCLUSIONS: Clinicians in the study settings
requested information frequently. Many of these information needs required
the synthesis of patient information and medical knowledge and thus were
potentially difficult to satisfy. A typology is proposed that
characterizes information needs as consciously recognized, unrecognized,
and currently satisfied. Copyright Annals of Internal Medicine; <A
"http://www.acponline.org/">http://www.acponline.org/</A>.</P><A
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<HR>
<UL>
<LI><STRONG><A name=4b>Vocabulary Analysis and Merging</A></STRONG>
</LI></UL>
<HR>
<P>Bicknell EJ, Sneiderman CA, Rada RF. Computer-assisted merging and
mapping of medical knowledge bases. Proc Annu Symp Comput Appl Med Care
1988:158-64. A user-interactive rule-based computer program, developed for
the purpose of mapping and merging multiple hierarchical thesauri, is
described. The program, called DynaSaurI (dynamic thesaurus integration),
was tested on subsets of two medical thesauri, the Systemized Nomenclature
of Medicine (SNOMED) and the Medical Subject Headings (MeSH). Each
thesaurus is treated as a knowledge base, containing information both in
the terms and in the various types of relationships between terms.
DynaSaurI uses combinations of string matching and tree browsing to
propose a ranked array of related MeSH terms for each SNOMED term
presented. A medical expert selected the closest match from the array of
terms proposed by DynaSaurI and entered the appropriate type of
relationship between the terms. The information acquired from the expert
was then used to refine DynaSaurI's mapping rules. With DynaSaurI, all 84
SNOMED concepts were successfully merged with and mapped to MeSH main
headings; 74(88%) were mapped by the initial DynaSaurI pass, and the
remainder by incorporating the user's responses. All merging utilized the
relationship descriptions (e.g., "is narrower than") provided by the
online interaction with the medical expert. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>From the president: reviewing nursing concepts to be included in the
1995 version of the Unified Medical Language System. Nurs Diagn 1995
Apr-Jun;6(2):53-4.</P>
<P>Kannry JL, Wright L, Shifman M, Silverstein S, Miller PL. Portability
issues for a structured clinical vocabulary: mapping from Yale to the
Columbia medical entities dictionary. J Am Med Inform Assoc 1996
Jan-Feb;3(1):66-78. To examine the issues involved in mapping an existing
structured controlled vocabulary, the Medical Entities Dictionary (MED)
developed at Columbia University, to an institutional vocabulary, the
laboratory and pharmacy vocabularies of the Yale New Haven Medical Center.
200 Yale pharmacy terms and 200 Yale laboratory terms were randomly
selected from database files containing all of the Yale laboratory and
pharmacy terms. These 400 terms were then mapped to the MED in three
phases: mapping terms, mapping relationships between terms, and mapping
attributes that modify terms. 73% of the Yale pharmacy terms mapped to MED
terms. 49% of the Yale laboratory terms mapped to MED terms. After certain
obsolete and otherwise inappropriate laboratory terms were eliminated, the
latter rate improved to 59%. 23% of the unmatched Yale laboratory terms
failed to match because of differences in granularity with MED terms. The
Yale and MED pharmacy terms share 12 of 30 distinct attributes. The Yale
and MED laboratory terms share 14 of 23 distinct attributes. The mapping
of an institutional vocabulary to a structured controlled vocabulary
requires that the mapping be performed at the level of terms,
relationships, and attributes. The mapping process revealed the importance
of standardization of local vocabulary subsets, standardization of
attribute representation, and term granularity. Copyright by and reprinted
with permission of the American Medical Informatics Association.</P>
<P>Lowe HJ, Barnett GO. Understanding and using the medical subject
headings (MeSH) vocabulary to perform literature searches. JAMA 1994 Apr
13;271(14):1103-8. Comment in: JAMA 1995 Jan 18;273(3):184; discussion
184-5.</P>
<P>Masarie FE Jr, Miller RA. Medical Subject Headings and medical
terminology: an analysis of terminology used in hospital charts. Bull Med
Libr Assoc 1987 Apr;75(2):89-94. Terminology used by health professionals
in everyday written discourse was compared with terminology in a
standardized medical vocabulary, the Medical Subject Headings (MeSH).
Fifty written hospital charts were selected at random and analyzed by a
computer program that identified MeSH terms in the charts. The charts were
analyzed against two related MeSH vocabularies- one containing MeSH terms
and one containing both MeSH terms and backwards cross-reference terms.
when small words such as articles and prepositions were disregarded,
approximately 50% of the words in a medical chart were found to be
MeSH-related terminology. In addition, about 40% of MeSH-related words in
the charts were either MeSH terms or backwards cross-reference terms.
Copyright by and reprinted with permission of the Medical Library
Association.</P>
<P>McCray AT, Browne AC, Moore DL. The semantic structure of neo-classical
compounds. Proc Annu Symp Comput Appl Med Care 1988:165-8. The automated
analysis of neo-classical compounds in the medical domain has been
proposed and carried out by a number of researchers in recent years. This
paper discusses the semantics of these compounds. The results indicate
that neo-classical compounds are semantically underdetermined by their
constituent parts. Thus, automated analysis of these compounds will need
to be supplemented by human review. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Miller PL, Smith P, Morrow JS, Riely CA, Powsner SM. Semantic
relationships and MeSH. Proc Annu Symp Comput Appl Med Care 1988:174-9.
This paper compares bibliographic retrieval using current MeSH (Medical
Subject Headings) to bibliographic retrieval using explicitly coded
semantic relationships between index terms. In a previous study, 10 lists
of abstracts, each list containing 20-40 papers discussing a specific pair
of terms, were analyzed to identify the specific relationship(s) between
those terms discussed in each paper. In the present study, we analyze how
well current MeSH coding, using topical subheadings and check tags, can
selectively retrieve those papers discussing each semantic relationship.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=4c>Knowledge Acquisition and
Representation</A></STRONG> </LI></UL>
<HR>
<P>Ball S, Wright L, Miller P. SENEX, an object-oriented biomedical
knowledge base. Proc Annu Symp Comput Appl Med Care 1989:85-9. An
object-oriented knowledge base, SENEX, in the domain of neurodegeneration
and loss of memory in aging is being developed. Initially, the focus is on
three sets of issues in the representation of biomedical information.
First, the authors are seeking to extend the medical subject headings
(MeSH) nomenclature to include new classes of biomedical entities and to
include relationships among those entities. Second, they are structuring
biomedical information rather than categorizing text for bibliographic
retrieval. Third, they are exploring ways in which such information could
be used in an interactive system created for purposes of education and for
designing basic research experiments. The current behavior of SENEX, which
is being developed using the Common Lisp Object System (CLOS), is
described. Various issues raised and plans for future development are
discussed. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Ball SS, Mah VH, Miller PL. SENEX: a computer-based representation of
cellular signal transduction processes in the central nervous system.
Comput Appl Biosci 1991 Apr;7(2):175-87. The SENEX project is exploring
knowledge representation in the neurobiology of ageing through
object-oriented programming. SENEX is built from a classification
structure of biologic entities and significant relationships among them.
For example, an enzyme is an entity and an enzymatic reaction is a
relationship among enzyme, cofactor(s), substrate(s) and product(s). There
are currently 2600 classes of entities and 50 classes of relationships in
SENEX. The class structure serves several functions. One function is to
interrelate general and specific categories of molecular and morphologic
entities. For example, tyrosine kinase and serine/threonine kinase are
specific types of the more general class of protein kinase enzymes.
Another function of the class structure is to serve as a network through
which inheritance of attributes may occur. For example, the attribute
'subunits' is inherited by all subclasses of the general class
multisubunit protein. Information may be accessed through links
established in the class structure and through links relating one object
as part of another. Relationships form the basis of separate modules
within SENEX. This paper describes the types of relationships currently
used and planned in the representation of age-related changes in cellular
signal transduction processes of mammalian central nervous systems. We
also describe tools for specific retrieval of relationships and for
tracing links in complex reaction cascades. Application of these tools to
identifying possible signal transduction pathways to guide further
exploration through experimentation is discussed. Reprinted by permission
of Oxford University Press.</P>
<P>Barr CE, Komorowski HJ, Pattison-Gordon E, Greenes RA. Conceptual
modeling for the unified medical language system. Proc Annu Symp Comput
Appl Med Care 1988:148-51. The Unified Medical Language System was
proposed by the National Library of Medicine to facilitate the exchange
and utilization of information from multiple sources. We are using
semantic networks as the knowledge representation scheme in a prototype
system to explore how to accomplish these goals. Conceptual modeling helps
define a complete and consistent set of objects and relationships to
include in the semantic net. Both top-down and bottom-up approaches were
found useful in the seven step process of building the semantic network.
Theoretical and practical issues are discussed as well as future
extensions to the current prototype. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Berman L, Cullen M, Miller PL. Automated integration of external
databases: a knowledge-based approach to enhancing rule-based expert
systems. Comput Biomed Res 1993 Jun;26(3):230-41. Expert system
applications in the biomedical domain have long been hampered by the
difficulty inherent in maintaining and extending large knowledge bases. We
have developed a knowledge-based method for automatically augmenting such
knowledge bases. The method consists of automatically integrating data
contained in commercially available, external, online databases with data
contained in an expert system's knowledge base. We have built a prototype
system, named DBX, using this technique to augment an expert system's
knowledge base as a decision support aid and as a bibliographic retrieval
tool. In this paper, we describe this prototype system in detail,
illustrate its use, and discuss the lessons we have learned in its
implementation. Copyright 1993 Academic Press.</P>
<P>Berman L, Cullen MR, Miller PL. Automated integration of external
databases: a knowledge-based approach to enhancing rule-based expert
systems. Proc Annu Symp Comput Appl Med Care 1992:227-33. Expert system
applications in the biomedical domain have long been hampered by the
difficulty inherent in maintaining and extending large knowledge bases. We
have developed a knowledge-based method for automatically augmenting such
knowledge bases. The method consists of automatically integrating data
contained in commercially available, external, on-line databases with data
contained in an expert system's knowledge base. We have built a prototype
system, named DBX, using this technique to augment an expert system's
knowledge base as a decision support aid and as a bibliographic retrieval
tool. In this paper, we describe this prototype system in detail,
illustrate its use and discuss the lessons we have learned in its
implementation. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Canfield K, Bray B, Huff S. Representation and database design for
clinical information. Proc Annu Symp Comput Appl Med Care 1990:350-3.
Semantic discourse analysis and sublanguage methods are used to create a
database model from free-text echocardiography reports. This model
dictates the object structure of a sematic model that is implemented in a
relations database form and evaluated for representational adequacy. The
sematic frame structure of this relational patient database is a flexible
projection of a hierarchical dictionary. The Unified Medical Language
System (UMLS) Metathesaurus could be used as such a dictionary. The result
is a structured clinical report database model that is built on a standard
dictionary and is generalizable to other domains. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Canfield KC, Bray BE, Huff SM, Warner HR. Database capture of natural
language echocardiographic reports: A UMLS approach. Proc Annu Symp Comput
Appl Med Care 1989:559-63. We describe a prototype system for
semiautomatic database capture of free-text echocardiography reports. The
system is very simple and uses a Unified Medical Language System
compatible architecture. We use this system and a large body of texts to
create a patient database and develop a comprehensive hierarchical
dictionary for echocardiography. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Chang S-Y. Kanes: knowledge acquisition for a neuroradiology expert
system [dissertation]. [Salt Lake City]: The University of Utah; 1991. 151
p. Available from: University Microforms, Ann Arbor, MI; 9133706. One of
the most severe obstacles to applying medical informatics to solve
practical medical problems is acquiring the knowledge base. The Iliad
knowledge base is among the most comprehensive medical knowledge bases in
existence. The amount of effort devoted to its creation and maintenance is
a testimony to the difficulty of building academic-quality, comprehensive
knowledge bases for practical medical applications. In addition to the
difficulty of knowledge acquisition, the accuracy and reliability of
knowledge base are also major concerns for the developers and users of
Iliad expert system. The major emphasis of this project was to use a
patient database to improve the efficiency of creating a knowledge base
for the neuroradiology domain and increase the accuracy of Iliad expert
system based on this knowledge base. The project introduced a knowledge
engineering model to automatically generate disease profiles in
neuroradiology. The model used a new technique to collect patient data,
obtain important statistics, calculate finding utility, and extract the
best findings for the diagnostic frames. Knowledge Acquisition for a
Neuroradiology Expert System (KANES) is an efficient, accurate, and
easy-to-use personal computer program that can assist knowledge engineers
in managing the patient database and executing the analysis tasks
described above. The experience with the KANES program using a relational
Database Management System (DBMS) can be extended to a larger environment
where information is gathered from multiple sources and where real-time
decisions need to be made. The knowledge engineering session in the
Department of Medical Informatics is a good example of such an environment
where different categories of individuals need and generate information
and make decisions related to teaching, research, management, and
administration. Under contract from the Unified Medical Language System
(UMLS) project of the National Library of Medicine, a database is being
built to contain clinical data from multiple sources like QMR, HELP, and
Iliad. As the quality of the data in medical information systems improves,
such databases will become an important resource for all of the
probabilities that drive computerized diagnostic systems. The KANES
program has the potential to expand to be a decision support system for
all medical domains that would help the groups in the knowledge
engineering session to make decisions more easily and more appropriately.
Provided by UMI.</P>
<P>Cimino JJ, Elkin PL, Barnett GO. As we may think: the concept space and
medical hypertext. Comput Biomed Res 1992 Jun;25(3):238-63. Hypertext, a
medium for presenting written material in a nonsequential manner, is
gaining popularity as a format for medical text. The structure of
traditional hypertext documents (hyperdocuments) includes author-created
links among text segments. This structure poses challenge for those who
create and maintain hyperdocuments, while reading them can introduce
disorientation and cognitive overload. An alternative model is presented
in which text segments are linked to the concepts which they contain and
the concepts are linked to each other in a semantic network called the
Concept Space. The concepts and semantic links attempt to approximate
potential topics of interest, allowing the reader to browse the
hyperdocument in an individualized manner, rather than in an
author-designated one. The concept space approach offers advantages for
both the author and the reader. Copyright 1992 Academic Press.</P>
<P>Cimino JJ, Mallon LJ, Barnett GO. Automated extraction of medical
knowledge from Medline citations. Proc Annu Symp Comput Appl Med Care
1988:180-4. The Medline database consists of over six million citations to
the medical literature, indexed by the National Library of Medicine with
the use of Medical Subject Headings (MeSH) and Subheadings. We propose
that analysis of MeSH Headings and Subheadings in Medline citations will
reveal the interrelationships among medical concepts described in the
original articles. We have developed a rule-based system which postulates
relationships based on the co-occurrence of MeSH Headings in Medline
citations. At present, the rule base consists of 504 rules which propose
57 relationships. When this rule base was applied to a test of 673
citations, 93% of the proposed relationships were determined to be correct
(96%, after correction of a transcription error in the rule base). We
believe this approach has great potential, both for assisting acquisition
of medical knowledge and for improving the quality of Medline retrievals.
Copyright by and reprinted with permission of the American Medical
Informatics Association.</P>
<P>Elkin PL, Cimino JJ, Lowe HJ, Aronow DB, Payne TH, Pincetl PS, Barnett
GO. Mapping to MeSH (the art of trapping MeSH equivalence from within
narrative text). Proc Annu Symp Comput Appl Med Care 1988:185-90. A tool
for identifying medical subject headings (MeSH) terms found in narrative
text is evaluated and discussed. The system's task is to discern unique
matches from within MeSH for noun phrases in narrative text. The program
consists of a medical morphological reduction routine, coupled with data
structures created for the MeSH vocabulary searcher, MicroMeSH. To
evaluate this tool, a study was undertaken within which three physicians
were asked to review citations from the Annals of Internal Medicine and
three paragraphs from a Textbook of Cardiology. They were asked to
identify all of the important medical concepts within both the citations
and text. Then these same physicians used MicroMeSH, to see which of these
medical concepts could be mapped to MeSH. These results were compared to
the output of our automated system. Of the concepts which were found to be
medical concepts by our panel of experts 89% were identified using
MicroMeSH as being represented in MeSH. The automated system was able to
translate 90% of those medical concepts to the same MeSH term as
identified by MicroMeSH. The remaining 10% of the concepts, which were
recognized by the experts and not by the system, were terms where the
medical knowledge of the experts allowed them to find matches which had no
representation, morphologically or through an Entry Term, in the MeSH
vocabulary. The specific algorithms, details of evaluation and potential
usefulness of the system are discussed. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Evans DA. Pragmatically-structured, lexical-semantic knowledge bases
for unified medical language systems. Proc Annu Symp Comput Appl Med Care
1988:169-73. Unified medical language systems must accommodate expressions
ranging from fixed-form standardized vocabularies to the free-text,
natural language of medical charts. Such ability will depend on the
identification, representation, and organization of the concepts that form
the useful core of the biomedical conceptual domain. The MedSORT-II and
UMLS Projects at Carnegie Mellon University have established a feasibile
design for the development of lexicons and knowledge bases to support the
automated processing of varieties of expressions (in the subdomain of
clinical findings) into uniform representations. The essential principle
involves incorporating lexical-semantic typing restrictions in a
pragmatically -structured knowledge base. The approach does not depend on
exhaustive knowledge representation, rather takes advantage of selective,
limited relations among concepts. In particular, the Projects have
demonstrated that practical, comprehensive, and accurate processing of
natural-language expressions is attainable with partial knowledge bases,
which can be rapidly prototyped. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Greenes RA, McClure RC, Pattison-Gordon E, Sato L. The
findings--diagnosis continuum: implications for image descriptions and
clinical databases. Proc Annu Symp Comput Appl Med Care 1992:383-7. As
part of the Unified Medical Language System (UMLS) project, we have been
exploring the use of semantic net representation to build a medical
ontology that can adapt to the needs and perspective of differing kinds of
users with varying purposes. A principal objective is to facilitate
indexing and retrieval of objects in a variety of target databases, using
their own source vocabularies, while maintaining the representation of
concepts to which these source vocabularies refer in a single consistent
form, so that retrievals that span resource types can be accommodated. In
addition, a particular area of deficiency of the existing UMLS
Metathesaurus is that of clinical findings, a part of the problem being
the multiple alternative views and granularity levels at which clinical
findings are described in different target databases. The problem is
particularly obvious when one examines the way in which image findings are
described, which may be at a purely perceptual level, or at varying levels
of aggregation into higher level observations or interpretations. We have
developed a recursive model for representing observations and
interpretations in a semantic net along a continuum of degree of
aggregation, that appears to lend itself well to adaptation to varying
perspectives. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Komorowski J, Barr CE, Pattison-Gordon E, Greenes RA. Knowledge
modeling for the Unified Medical Language System. In: Kangassalo H, Ohsuga
S, Jaakkola H, editors. Information modelling and knowledge bases.
Amsterdam: IOS; 1990. p. 313-17.</P>
<P>Masarie FE Jr, Miller RA, Bouhaddou O, Giuse NB, Warner HR. An
interlingua for electronic interchange of medical information: using
frames to map between clinical vocabularies. Comput Biomed Res 1991
Aug;24(4):379-400. The proliferation of medical knowledge has led to the
development of extensive dictionaries for electronically accessing
information resources. The task of standardizing terminology used for
electronic hospital records and for knowledge bases for medical expert
systems and indexing the medical literature cannot easily be met by
developing a single, monolithic official medical vocabulary. Developing a
monolithic vocabulary would require a massive effort, and its existence
would not guarantee its use by third-party payors, by practicing
clinicians, or by developers of electronic medical information systems.
Recognizing this, the National Library of Medicine (NLM) has begun to
develop the Unified Medical Language System (UMLS) as a means of promoting
electronic information exchange among systems with controlled
vocabularies. The authors describe a frame-based system developed as an
experimental approach to mapping between controlled clinical vocabularies.
Copyright 1991 Academic Press.</P>
<P>Miller PL, Barwick KW, Morrow JS, Powsner SM, Riely CA. Towards a
conceptual scema of medical knowledge: facilitating transition between
different computer-based forms of clinical information. In: Hammond WE.
Proceedings of the AAMSI Congress 88; 1988 May 5-7; San Francisco.
Washington (DC): American Association for Medical Systems and Informatics;
1988. p. 77-82.</P>
<P>Nelson SJ, Sheretz DD, Erlbaum MS, Tuttle MS. Representing medical
knowledge in the form of structured text. The development of current
disease descriptions. Proc Annu Symp Comput Appl Med Care 1989:66-70. As
part of the Unified Medical Language System (UMLS) initiative, about 900
diseases have been described using "structured text." Structured text is
words and short phrases entered under labelled contexts. Vocabulary is not
controlled. The contexts comprise a template for the disease description.
The structured text is both manipulable by machine and readable by humans.
Use of the template was natural, and only a few problems arose in using
the template. Instructions to disease description composers must be
explicit in definitions of the contexts. Diseases to be described are
chosen, after clustering related diseases, according to the distinctions
that physicians practicing in the area under question believe are
important. Limiting disease descriptions to primitive observations and to
entities otherwise described within the corpus appears to be both feasible
and desirable. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=4d>Information and Retrieval Techniques</A></STRONG>
</LI></UL>
<HR>
<P>Elkin PL, McLatchey J, Packer M, Hoffer E, Cimino C, Studney D, Barnett
GO. Automated batch searching of MEDLINE for DXplain. Proc Annu Symp
Comput Appl Med Care 1989:436-40. To obtain references for the diseases in
the DXplain database a generic search strategy was created and then
combined with a communication protocol for MEDLINE. The system's efficacy
has been tested on the concepts contained in the DXplain disease names.
The system takes the DXplain disease name and identifies MeSH Terms or
their equivalent from within this unstructured input. These terms are then
utilized to search MEDLINE. How the searches are constructed and the order
in which they are performed, depend upon a user defined script (protocol
for querying MEDLINE). These scripts can be run repetitively to cover
multiple concepts. This technique for searching MEDLINE was used to
download citations that will be used as references for diseases in the
DXplain Database. DXplain is a medical diagnostic aid program developed
and maintained at the MGH. The script used was a 28 step algorithm which
was designed to download the most recent review articles about each of the
DXplain diseases. The system provides the user with the ability to specify
the number of articles which he/she would like returned from MEDLINE. This
paper describes the technique by which the articles were retrieved, as
well as the review process and the success rate of the system in
identifying appropriate articles. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Miller PL, Barwick KW, Morrow JS, Powsner SM, Riely CA. Semantic
relationships and medical bibliographic retrieval: a preliminary
assessment. Comput Biomed Res 1988 Feb;21(1):64-77. This paper describes a
project exploring whether semantic relationships between bibliographic
terms may effectively partition the clinical literature. To address this
question, a set of semantic relationships was identified between pairs of
bibliographic terms taken from four categories: (1) diseases, (2)
treatments, (3) tests, and (4) patient characteristics. The MEDLINE system
of the National Library of Medicine was used to generate lists of
abstracts relating to pairs of clinical terms. Each list of abstracts was
examined to identify the semantic relationships, if any, which applied to
the two terms in each paper. The study suggests that semantic
relationships may play a potentially valuable role in assisting
computer-based medical bibliographic retrieval. The degree to which
relationships partition the literature is strongly dependent on the
underlying semantics of the particular bibliographic terms involved.
Copyright 1988 Academic Press.</P>
<P>Miller PL, Morrow JS, Powsner SM, Riely CA. Semantically assisted
medical bibliographic retrieval: an experimental computer system. Bull Med
Libr Assoc 1988 Apr;76(2):131-6. An experimental computer-based
bibliographic retrieval system has been implemented to explore how
semantic (conceptual) relationships between MeSH terms might assist the
retrieval process. To construct the experimental system's database, lists
of abstracts were produced using MEDLINE. Each list contained papers
discussing a specified pair of terms. Each abstract was then analyzed to
determine the specific relationship(s) between the two terms discussed in
that paper. The project then explored how these semantic relationships
could be incorporated into the computer to enhance bibliographic
retrieval. Copyright by and reprinted with permission of the Medical
Library Association.</P>
<P>Miller PL, Smith P, Morrow JS, Riely CA, Powsner SM. Capturing the
semantic relationship between clinical terms with current MeSH
bibliographic coding. Comput Methods Programs Biomed 1988
Nov-Dec;27(3):205-11. This paper compares bibliographic retrieval using
current MeSH (Medical Subject Headings) to bibliographic retrieval using
explicitly coded semantic relationships between index terms. In a previous
study, ten lists of abstracts, each list containing 20-40 papers
discussing a specific pair of terms, were analyzed to identify the
specific relationship(s) between those terms discussed in each paper. In
the present study, we analyze how well current MeSH coding using topical
subheadings and check tags, can selectively retrieve those papers
discussing each semantic relationship.</P>
<P>Powsner SM, Barwick KW, Morrow JS, Riely CA, Miller PL. Coding semantic
relationships for medical bibliographic retrieval: a preliminary study.
Proc Annu Symp Comput Appl Med Care 1987:108-12. It is suggested that the
coding of semantic relationships may permit more precise searches of the
medical literature than conventional key/index term coding with Boolean
operators for retrieval. Such semantic coding captures the distinction
between papers concerned with how hepatitis B (HB) may cause/predispose to
liver neoplasms (LN) and papers concerned with how HB may effect outcome
in patients with LN. These distributions were demonstrated by retrieving
sets of MEDLINE abstracts, each set relevant to two clinical terms. Each
abstract was then reviewed to determine the implied semantic
relationship(s) between the two terms. Even in the restricted realm of
liver diseases a number of very different relationships between terms are
addressed in the literature. In addition, coding 'no relationship' allows
articles discussing LN and HB independently to be avoided. It is concluded
that semantic-relationship coding may prove to be very helpful for
retrieving concise reference lists, to support clinical decisions.
Copyright 1987 IEEE. Reprinted, with permission.</P>
<P>Radow DP, Blake M, Howard E, Jones C, Milgrom L, Ostergard M, Shaffer
E. Using the Metathesaurus for bibliographic retrieval: a
pre-implementation study. Proc Annu Symp Comput Appl Med Care
1994:980.</P><A
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<HR>
<UL>
<LI><STRONG><A name=4e>Vocabulary Browsers</A></STRONG> </LI></UL>
<HR>
<P>Appel RD, Komorowski HJ, Barr CE, Greenes RA. Intelligent focusing in
knowledge indexing and retrieval - the relatedness tool. Proc Annu Symp
Comput Appl Med Care 1988:152-7. Most present day information retrieval
systems use the presence or absence of certain words to decide which
documents are appropriate for a user's query. This approach has had
certain successes, but it fails to capture relationships between concepts
represented by the words, and hence reduces the potential specificity of
both indexing and searching of documents. A richer representation of the
semantics of documents and queries, and methods for reasoning about these
representations, have been provided by artificial intelligence.
Navigational tools for browsing and authoring knowledge bases (KB's) add a
convenient technique for focusing in the complex landscape of semantic
representations. The center of such representations is usually a frame or
a semantic network system. We are developing a prototype Unified Medical
Language System (UMLS) taxonomy to represent objects and relationships in
medicine. One focus of our research is improved methods for indexing and
querying repositories of biomedical literature. The technique which we
propose is based on the notion of relatedness of concepts. To this end we
define heuristics which find related concepts and apply it to the UMLS
taxonomy. Preliminary results from experiments with the implemented
heuristics demonstrate its potential usefulness. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Komorowski HJ, Greenes RA, Barr C, Pattison-Gordon E. Browsing and
authoring tools for a Unified Medical Language System. In: User-oriented
content-based text and image handling. RIAO 88 Program. Conference with
Presentation of Prototypes and Operational Demonstrations; 1988 Mar 21-24;
Cambridge, MA. Paris: C.I.D.; 1988. p. 624-41.</P>
<P>Komorowski HJ, Greenes RA, Pattison-Gordon E. The use of fisheye views
for displaying semantic relationships in a medical taxonomy. Proc Annu
Symp Comput Appl Med Care 1987:113-6. One of the critical issues for
development of the unified medical language system (UMLS), or taxonomy of
medical terms, is the identification of semantic features and
relationships that should be represented in the UMLS and the design of the
appropriate structure for storing and displaying these features and
relationships. One approach, the use of the 'fisheye view' for displaying
a region of interest in a semantic network, is discussed. This approach
narrows the field of view at any given time to include only the most
important and immediate 'landmarks', or items. Any of the se could then be
focused on, or another level of detail accessed. Copyright 1987 IEEE.
Reprinted, with permission.</P>
<P>Lowe H, Barnett GO, Scott J, Mallon L, Ryan-Blewett D. Remote Access
MicroMeSH: demonstration of an enhanced microcomputer system for searching
the MEDLINE database. Proc Annu Symp Comput Appl Med Care 1989:1009-11.
Remote Access MicroMeSH (RAMM) is a powerful but easy to use microcomputer
system for searching the medical literature. RAMM uses MicroMeSH, a system
for accessing the National Library of Medicine's (NLMs) Medical Subject
Headings (MeSH) vocabulary, to facilitate offline creation and refinement
of highly specific MEDLINE search queries. Using these queries, RAMM
automatically searches and retrieves citations from the MEDLINE databases
through the NLMs MEDical Literature Analysis and Retrieval System
(MEDLARS). As search query creation and citation review are performed
offline, the cost of online searching is minimized. Copyright by and
reprinted with permission of the American Medical Informatics
Association.</P>
<P>Lowe HJ, Barnett GO. MicroMeSH: a microcomputer system for searching
and exploring the National Library of Medicine's Medical Subject Headings
(MeSH) vocabulary. Proc Annu Symp Comput Appl Med Care 1987:717-20.
MicroMeSH is a microcomputer-based tool for searching and exploring a
complete, keyworded version of the National Library of Medicine's Medical
Subject Headings (MeSH) vocabulary. MeSH is used to index the MEDLINE
database. MicroMeSH allows the user to retrieve MeSH headings rapidly,
using either a powerful search operation or a user-friendly MeSH Tree
Walker. MicroMeSH can translate many commonly used biomedical terms to
equivalent MeSH headings. The program also provides access to the MeSH
subheadings vocabulary. The authors describe the operation of MicroMeSH
and the computer hardware required to use the system. Copyright 1987 IEEE.
Reprinted, with permission.</P>
<P>Lowe HJ, Barnett GO, Scott J, Mallon L, Blewett DR. Remote Access
MicroMeSH: evaluation of a microcomputer system for searching the MEDLINE
database. Proc Annu Symp Comput Appl Med Care 1989:445-7. Remote Access
MicroMeSH (RAMM) is a powerful but easy-to-use microcomputer system for
searching the MEDLINE database. RAMM incorporates MicroMeSH, a
microcomputer implementation of the National Library of Medicine's (NLMs)
Medical Subject Headings (MeSH) vocabulary. RAMM facilitates the creation
of highly specific MEDLINE search queries. The goals in creating RAMM were
to provide a system that could be used to search the medical literature
and to teach the basic skills required to use MeSH and MEDLINE. During the
past two years RAMM has been used by clinicians, library professionals,
researchers, and students at Harvard Medical School and at selected
academic sites in the US and Canada. In February of 1989, an effort to
formally evaluate RAMM was begun. This paper describes the preliminary
results of that evaluation. Copyright by and reprinted with permission of
the American Medical Informatics Association.</P><A
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<HR>
<UL>
<LI><STRONG><A name=4f>Research Tools</A></STRONG> </LI></UL>
<HR>
<P>Fu LS. A public domain unified medical language system (UMLS) patient
database (hospital information systems, event definition structures)
[dissertation]. [Salt Lake City]: The University of Utah; 1992. 132 p.
Available from: University Microforms, Ann Arbor, MI; 9236271. This
document has presented a research work under the Unified Medical Language
System (UMLS) design and its conceptual framework as well as its
experimental implementation has been introduced. Three hypotheses have
been proposed and tested with real patient cases from two hospital
information systems (HELP and VA). Primary conclusions of this work were:
(1) The total number of MOI entries will not grow indefinitely. For a
given domain, it tends to level-off as more data sources are added. (2) To
date, Event Definition structures can correctly represent a selected
subset of dictionary entries ranging from 83% to 99%. (3) The current
automatic instantiation algorithm has proven to have an 87% success rate.
(4) From the evidence shown using this prototype with the UMLS patient
database, it is possible to combine electronic patient records from
different patient information systems into a unified structure. Moreover,
this prototype allows the user to visually inspect the distribution of
relevant medical variables which demonstrates discrimination between
disease and nondisease groups independent of the source of data. Also,
several vital future enhancements were also discussed. Provided by
UMI.</P>
<P>Fu LS, Bouhaddou O, Huff SM, Sorenson DK, Warner HR. Toward a public
domain UMLS patient database. Proc Annu Symp Comput Appl Med Care
1990:170-4. The paper describes a unified structure with an associated
vocabulary to represent and store patient cases derived from different
computerized patient databases. The unified structure is based on the
concept of event definitions which are generic templates for representing
clinical data in a patient database. An implementation of this structure
has been evaluated using patient cases from two expert system (Iliad and
QMR) and a hospital information system (HELP). The primary focus of the
UMLS patient database is to accumulate patient information from different
sources and provide enhanced statistical estimates of clinically important
variables. Inter-communication and navigation among medical information
systems are other potential benefits of this unified computerized medical
record system. Copyright by and reprinted with permission of the American
Medical Informatics Association.</P>
<P>Fu LS, Huff S, Bouhaddou O, Bray B, Warner H. Estimating frequency of
disease findings from combined hospital databases: a UMLS project. Proc
Annu Symp Comput Appl Med Care 1991:373-7. Merging data from the Salt Lake
VA hospital database and the LDS hospital HELP system into a UMLS
sponsored unified patient database has demonstrated that distribution of
variables within a disease is hospital independent. Although disease
prevalence is clearly not the same among hospitals, analysis of data
within a disease group across hospitals can be done using such a merged
database. This unified patient database would allow study of unusual
diseases not possible using data from a single institution. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Schuyler PL, McCray AT, Schoolman HM. A test collection for
experimentation in bibliographic retrieval. Medinfo 1989;6(Pt 2):910-12.
To establish an environment in which various search and retrieval
experiments can be performed, a subset of MEDLINE, the National Library of
Medicine's bibliographic database, has been created according to the
following requirements: all citations have a 1986 journal publication
year, are in English, and have an author-prepared abstract. The resulting
file contain approximately 167000 citations. This is a reasonable size
that satisfies several necessary conditions for conducting search and
retrieval experiments. Accompanying this file are approximately one
hundred and fifty questions asked by users of the MEDLINE database and
approximately three thousand citations retrieved from the experimental
file in response to these queries. Assessments of the relevance of the
retrieved citations to the questions asked are also available.</P><A
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contents</A>
<HR>
<H2><A name=5>The UMLS in Relation to Other Programs</A></H2>
<HR>
<P>Cimino JJ. Review paper: coding systems in health care . Methods Inf
Med 1996 Dec;35(4-5):273-84. Computer-based patient data which are
represented in a coded form have a variety of uses, including direct
patient care, statistical reporting, automated decision support, and
clinical research. No standard exists which supports all of these
functions. Abstracting coding systems, such as ICD, CPT, DRGs and MeSH
fail to provide adequate detail, forcing application developers to create
their own coding schemes for systems. Some of these schemes have been put
forward as possible standards, but they have not been widely accepted.
This paper reviews existing schemes used for abstracting, electronic
record systems, and comprehensive coding. It also discusses the remaining
impediments to acceptance of standards and the current efforts to overcome
them, including SNOMED, the Gabrieli Medical Nomenclature, the Read
Clinical Codes, GALEN, and the Unified Medical Language System (UMLS).</P>
<P>Cimino JJ, Sengupta S. IAIMS and UMLS at Columbia-Presbyterian Medical
Center. Med Decis Making 1991 Oct-Dec;11(4 Suppl):89S-93S. The authors use
an example to illustrate combining Integrated Academic Information
Management System (IAIMS) components (applications) into an integral
whole, to facilitate using the components simultaneously or in sequence.
They examine a model for classifying IAIMS systems, proposing ways in
which the Unified Medical Language System (UMLS) can be exploited by them.
Copyright 1991 Hanley and Belfus.</P>
<P>Frawley SJ. Building a Database of Data Sets for Health Services
Research. Proc Annu Symp Comput Appl Med Care 1994:377-81. The Database of
Data Sets (DB/DS) for Health Services Research will be an online
searchable directory of data sets which are available, often with
restrictions and confidentiality safeguards, for use by health care
researchers. The DB/DS project is aimed at a wide audience, and intends to
include a very broad range of health care data sets, ranging from state
hospital discharge data bases, to national registries and health survey
data sets, to institutional clinical databases. The intended users are the
same community of researchers, policy-makers, administrators and
practitioners who are served by the National Library of Medicine's current
bibliographic databases. This paper describes a pilot phase of the DB/DS
project in which the issues involved in creating such a database were
explored with an initial set of 20 representative data sets. Copyright by
and reprinted with permission of the American Medical Informatics
Association.</P>
<P>Henry SB, Holzemer WL, Reilly CA, Campbell KE. Terms used by nurses to
describe patient problems: can SNOMED III represent nursing concepts in
the patient record? J Am Med Inform Assoc 1994 Jan-Feb;1(1):61-74.
OBJECTIVE: To analyze the terms used by nurses in a variety of data
sources and to test the feasibility of using SNOMED III to represent
nursing terms. DESIGN: Prospective research design with manual matching of
terms to the SNOMED III vocabulary. MEASUREMENTS: The terms used by nurses
to describe patient problems during 485 episodes of care for 201 patients
hospitalized for Pneumocystis carinii pneumonia were identified. Problems
from four data sources (nurse interview, intershift report, nursing care
plan, and nurse progress note/flowsheet) were classified based on the
substantive area of the problem and on the terminology used to describe
the problem. A test subset of the 25 most frequently used terms from the
two written data sources (nursing care plan and nurse progress
note/flowsheet) were manually matched to SNOMED III terms to test the
feasibility of using that existing vocabulary to represent nursing terms.
RESULTS: Nurses most frequently described patient problems as
signs/symptoms in the verbal nurse interview and intershift report. In the
written data sources, problems were recorded as North American Nursing
Diagnosis Association (NANDA) terms and signs/symptoms with similar
frequencies. Of the nursing terms in the test subset, 69% were represented
using one or more SNOMED III terms. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Integrated Academic Information Management Systems (IAIMS). Bull Med
Libr Assoc 1992 Jul;80(3):241-3. This paper reviews the proceedings of the
symposia sponsored by the Integrated Academic Information Management
Systems Association. IAIMS is described from the perspectives of
information management, knowledge management, and information technology.
Papers delivered at the symposia are reviewed. An overview of the National
Library of Medicine and the IAIMS initiative at NLM, the use of an IAIMS
project at Georgetown University to bring together multiple sources of
information, and the linking of an IAIMS system to the Unified Medical
Language System initiative at Yale are also discussed. Copyright by and
reprinted with permission of the Medical Library Association.</P>
<P>Lindberg DA. Global information infrastructure. Int J Biomed Comput
1994 Jan;34(1-4):13-9. The High Performance Computing and Communications
Program (HPCC) is a multiagency federal initiative under the leadership of
the White House Office of Science and Technology Policy, established by
the High Performance Computing Act of 1991. It has been assigned a
critical role in supporting the international collaboration essential to
science and to health care. Goals of the HPCC are to extend USA leadership
in high performance computing and networking technologies; to improve
technology transfer for economic competitiveness, education, and national
security; and to provide a key part of the foundation for the National
Information Infrastructure. The first component of the National Institutes
of Health to participate in the HPCC, the National Library of Medicine
(NLM), recently issued a solicitation for proposals to address a range of
issues, from privacy to 'testbed' networks, 'virtual reality,' and more.
These efforts will build upon the NLM's extensive outreach program and
other initiatives, including the Unified Medical Language System (UMLS),
MEDLARS, and Grateful Med. New Internet search tools are emerging, such as
Gopher and 'Knowbots'. Medicine will succeed in developing future
intelligent agents to assist in utilizing computer networks. Our ability
to serve patients is so often restricted by lack of information and
knowledge at the time and place of medical decision-making. The new
technologies, properly employed, will also greatly enhance our ability to
serve the patient.</P>
<P>Lindberg DA. The IAIMS opportunity: the NLM view. Bull Med Libr Assoc
1988 Jul;76(3):224-5.</P>
<P>McCormick KA, Zielstorff R. Building a Unified Nursing Language System
(UNLS). In. Nursing data systems: the emergency framework. Washington
(DC): American Nurses Publishing; 1995. p.143-9.</P>
<P>Paton JA, Belanger A, Cheung KH, Grajek S, Branch KA, Ikeda N, Sette L,
Miller PL, Fryer RK. Online bibliographic information: integration into an
emerging IAIMS environment. Proc Annu Symp Comput Appl Med Care
1992:605-9. The Medical Library at Yale University has developed an online
free-text database containing Current Contents citations. The database was
designed to be integrated into an emerging campus-wide information
environment. To this end Current Contents at Yale was designed with a user
interface familiar to the Yale community, an alerting service based on
electronic mail, and search expansion using the National Library of
Medicine's Meta-1 metathesaurus. Copyright by and reprinted with
permission of the American Medical Informatics Association.</P>
<P>Paton JA, Clyman JI, Lynch P, Miller PL, Sittig DF, Berson BZ.
Strategic planning for IAIMS: prototyping as a catalyst for change. Proc
Annu Symp Comput Appl Med Care 1990:709-13. Yale School of Medicine has
developed a prototype integrated computing and information environment as
part of its strategic IAIMS planning. The prototype consists of a menu
system and underlying network communications programs and networks to
access a variety of medical information resources at Yale and elsewhere.
This prototype has been used in testing user needs, in designing a
technical architecture, in exploring related institutional issues, and as
a basis for research in integrated access to medical information using
UMLS tools and concepts. Copyright by and reprinted with permission of the
American Medical Informatics Association.</P>
<P>Roderer NK. Dissemination of medical information: organizational and
technological issues in health sciences libraries. Libr Trends 1993
Summer;42(1):108-26. This article describes five programs that have been
particularly significant to the evolution of biomedical communications
over the last twenty years: the National Network of Libraries of Medicine
(NNLM), Integrated Academic Information Management Systems (IAIMS),
National Research and Education Network (NREN), Unified Medical Language
System (UMLS), and the electronic journal. The major implications that
each of these programs will continue to have for health sciences
librarianship are examined. Reprinted with permission from Library Trends.
Copyright 1993 The Board of Trustees of the University of Illinois.</P>
<P>Scherrer JR. Medical languages: use, definition and processing in ward
information systems (WIS). In: Adlassnig KP, Grabner G, Bengtsson S,
Hansen R, editors. Medical informatics Europe 1991. Proceedings; 1991 Aug
19-22; Vienna, Austria. Berlin: Springer-Verlag; 1991. p. 19-27.</P>
<P>Scherrer JR. [New architectures destined for hospital computer networks
opening the medical world to more communication facilities of every kind].
Schweiz Med Wochenschr 1990 Dec 8;120(49):1866-71. (Fre). </P>
<P>Siegel ER. High priority research at NLM. In: Information: the
transformation of society. Proceedings of the 50th Annual Meeting of the
American Society for Information Science; 1987 Oct 4-8; Boston, MA.
Medford (NJ): Learned Information; 1987. p. 275-6. A growing body of
medically related machine-readable data of at least four types is
identified. These include: biomedical literature, clinical records,
medically relevant data banks, and knowledge bases. The development of a
unified medical language system (UMLS) is discussed. The use of artificial
intelligence techniques in diagnosis and management is explored.
Reproduced with permission of the American Society for Information
Science.</P>
<P>Smith KA. Medical information systems (National Library of Medicine
information services). Bull Am Soc Inf Sci 1986 Apr-May;12(4):17-8. This
description of information services from the National Library of Medicine
(NLM) highlights a new system for retrieving information from NLM's
databases (GRATEFUL MED); a formal Regional Medical Library Network;
DOCLINE; the Unified Medical Language System; and Integrated Academic
Information Management Systems. Research and development and the future
are discussed . Reproduced with permission of the American Society for
information Science.</P>
<P>Tilley CB. Medical databases and health information systems. Annu Rev
Inf Sci Tech 1990;25:313-82.</P><A
href="http://www.nlm.nih.gov/archive/20040831/pubs/cbm/umlscbm.html#list">Return to title
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<HR>
<H2><A name=6>Commentaries and Opinions about UMLS</A></H2>
<HR>
<P>Bishop CW. Alternate approaches to a UMLS. Med Decis Making 1991
Oct-Dec;11(4 Suppl):S99-102. A scheme for the continuing development of
Meta-1, a taxonomy of medical subjects based; on MeSH and other systems,
is described. The objective is a single, structured classification for
medical knowledge. Copyright 1991 Hanley and Belfus.</P>
<P>Bishop CW, Ewing P. Representing medical knowledge: reconciling the
present or creating the future? MD Comput 1992 Jul-Aug;9(4):218-25. Modern
technology has sparked the creation of computing systems that perform many
medically related tasks, but communication between these systems is
limited, in part by differences in the terminology used for various
purposes and in part by the changing nature of medical concepts. The
Unified Medical Language System represents an attempt to find a means of
translation between diverse knowledge systems. An alternative, which we
propose, is to agree on a knowledge base for the future and make use of
present accomplishments in moving toward that goal. Copyright 1992
Springer-Verlag.</P>
<P>Cimino JJ. Saying what you mean and meaning what you say: coupling
biomedical terminology and knowledge. Acad Med 1993 Apr;68(4):257-60.</P>
<P>Evans DA. Medical language processing: issues and methods in unifying
medical concepts: reflections on the UMLS project. In: Managing
information and technology. Proceedings of the 52nd Annual Meeting of the
American Society for Information Science; 1989 Oct 30-Nov 2; Washington,
DC. Medford (NJ): Learned Information; 1989. p. 252-3. Several
medical-related language processing projects are examined: (1) the UMLS
project, focusing on development of a "meta-thesaurus" for concepts in
biomedicine and an "information sources map" to coordinate access to
information across databases; (2) NYU's Medical Language Processor (MLP),
a 5-stage computer processing system which analyzes sentences so that
their informational elements are recognized and labeled for mapping into
the correct database field; and (3) the Systemized Nomenclature of
Medicine (SNOMED), which is a comprehensive indexing system for clinical
medicine. Reproduced with permission of the American Society for
Information Science.</P>
<P>Rudin JL. DART (Diagnostic Aid and Resource Tool): a computerized
clinical decision support system for oral pathology. Compendium 1994
Nov;15(11):1316, 1318, 1320 passim.</P>
<P>Tuttle MS, Nelson SJ. The role of the UMLS in 'storing' and 'sharing'
across systems. Int J Biomed Comput 1994 Jan;34(1-4):207-37. We will argue
that 'sharing', 're-use', 're-purposing', and 'addition' of health care
information is difficult, intrinsically; that the best way to overcome the
difficulty is to start doing it, as soon as possible, and that the UMLS
Knowledge Sources provide the best place to start. We recommend that the
UMLS be used as a default source of biomedical concept names and
relationships, as a comprehensive, data-based, 'reference model', and as
an example of a large, ecumenical, evolving, continuously updated source
of re-usable health care information.</P><A
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<P><!-- ************************* Content end ************************* -->
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<b>First published: </b>21 March 1997<br/><b>Last updated: </b>24 April 1998<br/><b>Date Archived: </b>31 August 2004<br/><a href="http://www.nlm.nih.gov/cgi/viewMeta.pl?url=http://www.nlm.nih.gov/archive//20040831/pubs/cbm/umlscbm.html&amp;description=full" onclick="javascript:openPopup('http://www.nlm.nih.gov/cgi/viewMeta.pl?url=http://www.nlm.nih.gov/archive//20040831/pubs/cbm/umlscbm.html&amp;description=full'); return false;"><strong>Metadata</strong></a> | <b> <a href="http://www.nlm.nih.gov/permlevels.html"onclick="javascript:openPopup('http://www.nlm.nih.gov/permlevels.html'); return false;">Permanence level</a>: </b>Permanent: Stable Content<br/>
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