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The KnowledgeMap project: development of a concept-based medical school curriculum database.

We developed the KnowledgeMap (KM) system as an online, concept-based database of medical school curriculum documents. It uses the KM concept indexer to map full-text documents and match search queries to concepts in the Unified Medical Language System (UMLS). In this paper, we describe the design of KM and report the first seven months of its implementation into a medical school. Despite being emphasized in only two first year courses and one fourth year course, students from all four classes used KM to search and browse documents. All faculty members involved with courses piloting KM used the system to upload and manage lecture documents. Currently, we are working with eight course directors to transition their courses to KM for next year.

Abstracting and Indexing↗

An application of Expert Network to clinical classification and MEDLINE indexing.

An effective and efficient learning method, Expert Network (ExpNet), is introduced in this paper. ExpNet predicts the related categories of an arbitrary text based on a search of its nearest neighbors in a set of training texts, and a reasoning from the expert-assigned categories of these neighbors. Evaluations in patient-record text classification and MEDLINE document indexing show a performance of ExpNet in recall and precision comparable to the Linear Least Squares Fit (LLSF) mapping method, and significantly better than other methods tested. We also observed that ExpNet is much more efficient than LLSF in computation. The total training and testing time on the patient-record text collection (6134 texts) was 4 minutes for ExpNet versus 96 minutes for LLSF; on the MEDLINE document collection (2344 documents), the total time was 15 minutes for ExpNet versus 4.6 hours for LLSF. It is evident in this study that human knowledge of text categorization can be statistically learned without expensive computation, and that ExpNet is such a solution.

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Description and advantages of an index-driven medical knowledge base.

In the FRAMEMED system design, the inherent attributes of its concepts are expressed in the hierarchical lists of its 26 Elements (e.g., Agents, Clinical Manifestations, Diseases, Tests, etc.). These concepts, contained in regular structures, are then alphabetized by phrase (and synonym), forming a combined index in which the user may quickly find a concept either alphabetically or hierarchically. Stored in the structures of the index are pointers to four types of knowledge records: 1) Descriptive (definition); 2) Relational (incidental attributes); 3) Conditional (rules); and 4) Procedural (how to). In contrast to the index which is stored in regular structures for rapid access (like relational databases), the knowledge records are stored in free text (variable length) and may include pointers to imaging and audio records. A particular feature of the FRAMEMED system is careful attention to modifiers, an aspect usually not emphasized in other systems. In trying to structure the free text describing a patient encounter, for example, the major concepts such as cough, fever, stiff neck, etc., are relatively easy to code (although a common system has not yet been agreed upon). The devil lies in the modifiers such as 'history of', 'severe,' 'constant,' 'absent,' 'left,' 'abnormal,' etc., particularly when there is concatenation of modifiers modifying modifiers. Our Relational records (in our knowledge base) and our Chronological Medical Records (CMR) in our patient record have the same format, namely, a title, several related items, and a date/author. For example, our disease profile (Relational record) for 'Influenza' might include 'cough,' 'fever,' and 'stiff neck.' The CMR of a particular patient encounter might include the same items. The only differences would be the title (disease name for the disease profile, date for the CMR, and the omission of the redundant date in the date/author line of the CMR). Each related item in either of these records is expressed in a four-part string, namely: 1) Relation; 2) Code; 3) Phrase; and 4) Comment. Modifiers (common ASCII symbols) are structured into each of these parts. For example, if the patient did not have 'cough,' the default '+' in the Relation would be edited to a '-', while 'history of' cough would be '>'. Each Relation can be graded (on a 5-level scale) for both importance and frequency. The Code for a test can carry the result suffix, '+ positive/high,' '-negative/low,' '# abnormal (qualitatively)', or '1 unremarkable/normal.' Topological information, such as '/left,' can be appended to a Code. If the cough is getting worse, its code can have the suffix, '<'. The standardized Phrases associated with the Codes come from the hierarchical lists of the index section described earlier. Phrases are not stored, being rematched to the codes as needed for user display. This practice not only saves memory space but allows a CMR encounter recorded in one language to be displayed in another second language subsequently, requiring only the existence of the hierarchical code/phrase in the second language. A free-text Comment is allowed for any related item in a Relational record or CMR, to allow the doctor to add important nuances such as 'worse on arising' or for a numeric result such as a test result or a thermometer reading. Some structuring can be accommodated in the Comment by introducing symbols such as '> relieved by,' followed by a list containing entries such as 'antacids.' Time can be sturctured through symbol lists such as '@-2 mo' representing '2 months previously.' Because Relational records in the knowledge ase and patient encoutner records in the CMR both display findings in hierarchical order; all similar items (e.g., Agents, Clinical Manifestations, Tests, Procedures, etc.) occur together and in an unique order. (abstract truncated)

Abstracting and Indexing↗

Evaluation of impact factor of the Indian Journal of Gastroenterology.

OBJECTIVE: a) To determine the impact factor (IF) of the Indian Journal of Gastroenterology (IJG) for the years 1987 to 1990. b) To compare the IF of the IJG with those of other gastroenterology journals. METHODS: For each year (1987 to 1990), the number of citations received in that particular year in the journals included in the Science Citation Index (SCI) phi by items published in the IJG in the previous two years was determined by manual searching of SCI. Similarly, self citations in the IJG of articles published in the IJG were determined manually from the back volumes of the journal. IF was calculated from these data. RESULTS: The IF of IJG for the years 1987, 1988, 1989 and 1990 was 0.087, 0.092, 0.098 and 0.192 respectively. The impact factor of IJG for 1990 compared quite poorly with that of other gastroenterology journals. CONCLUSIONS: The IF of IJG, though low, has shown a progressive improvement with time. Publication of better articles in the IJG should lead to improvement in its IF.

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Personal medical reference files for family physicians.

Family practice has firmly accepted a leadership role in the establishment of practice indexing and control mechanisms for primary care practices and in the continuing education of primary care physicians. These independent programs logically interrelate if the International Classification of Health Problems in Primary Care (ICHPPC) mobidity coding index is adapted to the maintenance of personal reference and bibliographic files. The literature data base so developed then was direct and specific application to patient care situations, and to continuing education oriented around active case material, teaching, and research. Experience demonstrates a high degree of student responsiveness to such a reference resourse. Yet most receive no exposure to this basic tool throughout their entire medical school and specialty training. An inexpensive, simple system is proposed which can be expanded conveniently to any level of detail, cross-reference capability, and content. This has been found useful in teaching and practice and is well accepted by family medicine residents at the Geisinger Medical Center.

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Concept-oriented indexing of video databases: toward semantic sensitive retrieval and browsing.

Digital video now plays an important role in medical education, health care, telemedicine and other medical applications. Several content-based video retrieval (CBVR) systems have been proposed in the past, but they still suffer from the following challenging problems: semantic gap, semantic video concept modeling, semantic video classification, and concept-oriented video database indexing and access. In this paper, we propose a novel framework to make some advances toward the final goal to solve these problems. Specifically, the framework includes: 1) a semantic-sensitive video content representation framework by using principal video shots to enhance the quality of features; 2) semantic video concept interpretation by using flexible mixture model to bridge the semantic gap; 3) a novel semantic video-classifier training framework by integrating feature selection, parameter estimation, and model selection seamlessly in a single algorithm; and 4) a concept-oriented video database organization technique through a certain domain-dependent concept hierarchy to enable semantic-sensitive video retrieval and browsing.

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Microfiche and automated indexing applications for regulatory submissions to the Food and Drug Administration.

In today's conservative climate, with cost-cutting consciousness, gradual steps should be taken to "marry" micrographics with new technologies. When managers have thorough knowledge and understanding of the regulatory requirements of the federal government, they can proceed to review, analyze and update documentation with indexing and decide the appropriate format of data, as well as the vehicles best suited for the user's needs, integrating micrographics and automated indexing. It is important that industry and regulatory agencies work together. For five years, Merck has been involved in refining microfiche specifications for submissions to various Bureaus at the Food and Drug Administration, originally for the Bureau of Drugs and currently for the Bureau of Foods and the Bureau of Veterinary Medicine. In these pilot projects, Merck has shared its know-how with other pharmaceutical companies in published articles, one-day seminars and several speeches at conferences of national organizations such as the Pharmaceutical Manufacturers Association (PMA) and the Association of Records Managers and Administrators (ARMA). In April 1979, a presentation was made before the Garden State Chapter of the National Micrographics Association (NMA).

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Indexing of medical diagnoses by word affinity method.

Automated coding of medical diagnoses is still an unsolved problem. Our goal in recent work was to find efficient, cheap and easy to implement method to assist the work of human encoders in hospitals. The proposed method is based on a vector-space model especially adapted to deal with short expressions, like clinical diagnoses. Using a set of coded diagnoses the co-occurrence of codes and words is more or less characteristic. The method describes these characteristics mathematically, by introduction of the so-called word adhesion. Two human encoders were asked to code the same set of 92 clinical diagnoses. Their results were compared to the ranked list of codes, produced by the computer. The results were better where the two human encoders agreed, and the overall results demonstrate the feasibility of the approach.

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Systematic review of medication errors in pediatric patients.

OBJECTIVE: To systematically locate and review studies that have investigated the incidence of medication errors (MEs) in pediatric inpatients and identify common errors. METHODS: A systematic search of studies related to MEs in children was performed using the following databases: MEDLINE (1951-April 2006), EMBASE (1966-April 2006), Pharm-line (1978-April 2006), International Pharmaceutical Abstracts (1970-April 2006), Cumulative Index to Nursing and Allied Health Literature (1982-April 2006), and British Nursing Index (1994-April 2006). Studies of the incidence and nature of MEs in pediatrics were included. The title, abstract, or full article was reviewed for relevance; any study not related to MEs in children was excluded. RESULTS: Three methods were used to detect MEs in the studies reviewed: spontaneous reporting (n = 10), medication order or chart review (n = 14), or observation (n = 8). There was great variation in the definitions of ME used and the error rates reported. The most common type of ME was dosing error, often involving 10 times the actual dose required. Antibiotics and sedatives were the most common classes of drugs associated with MEs; these are probably among the most common drugs prescribed. CONCLUSIONS: Interpretation of the literature was hindered by variation in definitions employed by different researchers, varying research methods and setting, and a lack of theory-based research. Overall, it would appear that our initial concern about MEs in pediatrics has been validated; however, we do not know the actual size of the problem. Further work to determine the incidence and causes of MEs in pediatrics is urgently needed, as well as evaluation of the best interventions to reduce them.

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Non-indexed medical journals in the Web: new perspectives in the medical literature.

Many medical journals, publishing in national languages, meet serious financial problems and difficulties when they attempt to become indexed in the international indices. Obviously, this not only affects the scientific quality of non-indexed medical journals (NIMJs) but also affects the awareness of the scientific community of topics with apparently local but potentially broader scientific significance. This is a reality for over 100 Greek medical journals, none of which has a life longer than 30 years or more than 2000 subscribers. Among them, the 'Archives of Hellenic Medicine' (AHM) is published and sponsored by the Athens Medical Society (the oldest medical society in Greece founded in 1835). This peer-reviewed Journal is being published for 13 years, bimonthly, in Greek. Attempting to overcome the above mentioned problems and to be involved in the process of discovering the most effective way of scientific 'skywriting', 2 years ago, the AHM entered full-text in the Web and it was decided that up to 500% of its volume should be covered by English-language papers. As a result, the AHM are now included in the main Web lists of medical journals and their home page is linked in many academic pages having approximately 500 hits/month. Furthermore, 45 retrievals of AHM's English-language papers or English abstracts of Greek-language articles were reported by e-mail response from abroad. Considered apart from the paper-publishing, the expenses of the digital publishing of the AHM are about half of those of paper-publishing, as they were before the appearance of the Journal in the Web. Up to now, about 40% of the Journal's digital publishing cost is covered by advertisements included in its pages and by a modification of its paper-publishing policy. It is concluded that the international scientific community is not indifferent for information published in NIMJs. Medical national minorities working abroad express special interest for this type of information. The Web makes the NIMJs accessible to these potential readers, who would never have the chance to acquire them in their printed form.

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Orthodontic literature: an overview of the last 2 decades.

The aim of this study was to explore the orthodontic literature in the most important orthodontic and other dental and medical journals from 1981 to 2000. The most commonly used medical bibliographic database, MEDLINE, was used. In addition, some journals were hand searched to estimate the error of the method. Despite some indexing inconsistencies, MEDLINE was found to be a powerful and relatively accurate tool for use in bibliometric studies. About 16,000 articles with orthodontic interest were published during this period. The number of orthodontic articles written in English rose during this period, but almost half of them (45%) were published in nonorthodontic journals. Articles in the orthodontic journals are focusing more and more on diagnosis and treatment evaluation as the need for high-quality evidence becomes obvious, while other topics, such as new techniques and new materials, are losing ground. Many high-quality studies with orthodontic interest are published in nonorthodontic journals with a high Impact Factor, remaining more or less out of reach for most orthodontists.

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Changes in rates of unscheduled hospital readmissions and changes in efficiency following the introduction of the Medicare prospective payment system. An analysis using risk-adjusted data.

The purpose of this study was to analyze changes in rates of unscheduled readmissions and changes in technical efficiency following the introduction of the Medicare Prospective Payment System (PPS). We developed the Risk-Adjusted Readmissions Index (RARI), which allowed us to make comparisons in rates of unanticipated readmissions across hospitals and over time. Data envelopment analysis (DEA), a linear programming technique, was used to measure changes in technical efficiency by comparing the inputs used and the outputs produced across a cohort of hospitals, while adjusting for changes over time in case mix and case complexity. Rates of unscheduled readmissions and efficiency scores were computed for a sample of 245 hospitals for each year. Although both readmission rates and efficiency scores increased for most hospitals, there was no evidence that those hospitals that experienced the greatest increases in efficiency had the largest increases in their rates of unscheduled readmissions.

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Automating terminological networks to link heterogeneous biomedical databases.

As cross-disciplinary research escalates, researchers are facing the challenge of linking disparate biomedical databases that have been developed without common indexes. Manually indexing these large-scale databases is laborious and often impractical. Solutions involving mediating terminologies have been proposed, but coordination of terms from the databases of interest to these mediating terminologies is also laborious, and regular synchronization between indexes is an additional problem. In this study we describe a novel method of linking heterogeneous databases using terminology networks constructed with automated mapping methods. Linkage was established between two disparate biomedical databases (SNOMED-CT and HDG), using two relevant intermediating databases (UMLS and OMIM). One gold standard of 514 distinct matches is used as proof-of-principle. In conclusion, as hypothesized, 1) Manually curated pathways provide high precision, but offer low recall, 2) the automated terminology pathways can significantly increase recall at acceptable precision. Taken together, our conclusion may suggest the combined manual and automated terminology networks could offer recall and precision in an incremental manner

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Latent Semantic Indexing of medical diagnoses using UMLS semantic structures.

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.

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[Growth and trends in scientific production in epidemiology in Brazil].

OBJECTIVES: To analyze the growth of epidemiological research in Brazil in comparison to the total number of indexed publications worldwide and from several Latin American and Caribbean countries. METHODS: A Boolean combination of epidemiological key words was used to search the MEDLINE/PubMed database for articles published between 1985 and 2004. These articles were divided into 4 time periods: 1985-9, 1990-4, 1995-9, and 2000-4. RESULTS: Of the total 211,727 articles identified in the MEDLINE/PubMed database, 1,952 (0.9%) were related to Brazil. The number of articles increased 12-fold throughout the period (from 91 to 1,096), and more than doubled (0.54% to 1.1%) if considered in relation to the total number of indexed articles. This growth was accompanied by diversification of the subjects addressed. The fields of infectious diseases and mother-child health, which predominated during the first period (74%), represented only a minority of articles in the last period. There was a noteworthy increase in the Brazilian output when compared to that of other Latin American and Caribbean countries. CONCLUSIONS: Our results corroborate previous evidence of the intense growth of epidemiological research in Brazil in the last two decades. This growth was more intense than mean growth worldwide, and much greater than that found in other Latin American countries. Therefore, Brazilian scientific output in the epidemiology field is showing a growth pattern similar to that of other scientific areas in the country.

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CINAHL list of subject headings: a nursing thesaurus revised.

The rationale and methods for revising the thesaurus of one of the major health sciences indexing tools are discussed. Computer production of the Cumulative Index to Nursing & Allied Health Literature and the possibility of online access mandated a revision of the list of subject headings. CINAHL has maintained a policy of responding to user needs and to changes in the nursing and allied health literature, and user input was encouraged during revision of the thesaurus. The methods of structural revision are described, and major changes in the thesaurus are detailed. Modification of the thesaurus is expected to have a far-reaching impact on the retrieval of information in nursing and allied health. Nursing and Allied Health (CINAHL) is now available online through DIALOG (file 218) and BRS (access code NAHL).

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Use of a computer software program for qualitative analyses--Part 1: Introduction to NUD.IST.

The NUD.IST (Non-numerical Unstructured Data Indexing, Searching, and Theorizing) program is recognized as one of the most efficient software programs for qualitative data analysis because it dramatically reduces the clerical tasks of cut and paste for coding and retrieval in text. However, little literature related to NUD.IST and its use in qualitative analysis is available to nurse researchers. Thus, the purposes of the first part of a two-part article are to describe the features of NUD.IST to nurse researchers and to present how NUD.IST was used in a qualitative study of dyspnea stimuli. In managing the qualitative data of dyspnea stimuli, NUD.IST 3.0 was effective in extracting, retrieving, and tracking text segments as well as identifying commonalties or patterns in data quickly.

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MeSHmap: a text mining tool for MEDLINE.

Our research goal is to explore text mining from the metadata included in MEDLINE documents. We present MeSHmap our prototype text mining system that exploits the MeSH indexing accompanying MEDLINE records. MeSHmap supports searches via PubMed followed by user driven exploration of the MeSH terms and subheadings in the retrieved set. The potential of the system goes beyond text retrieval. It may also be used to compare entities of the same type such as pairs of drugs or pairs of procedures etc. In addition there is the potential to generate maps of entities (drugs or diseases etc.) such that the strength of the link between two entities in the map represents their similarity as expressed in the MeSH metadata of the MEDLINE documents. Higher level operators have been proposed to support these comparison and mapping functions. This paper motivates and describes MeSHmap. Future work will include user evaluations of the system.

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