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Automatically identifying gene/protein terms in MEDLINE abstracts.

MOTIVATION: Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. RESULTS: GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. AVAILABILITY: A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

Abstracting and Indexing↗

The Unified Medical Language System (UMLS): integrating biomedical terminology.

The Unified Medical Language System (http://umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900,000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.

Animals↗

Evaluating the impact of a promotional campaign for screening mammography: women's knowledge and sources of awareness.

The Breast X-Ray Programme of the Central Sydney Health Service was advertised by generalised strategies aimed at the total community, including poster and pamphlet distribution, and strategies aimed at general practitioners, supplemented by written invitations and recommendation from the general practitioner, invitations for friends, and invitations from the service using the electoral listing. In order to evaluate the reach or impact of the promotional campaign in the Drummoyne local government area, telephone interviews were conducted with women aged 45 to 70 randomly selected from the community. Women's knowledge about breast cancer, screening and the Breast X-Ray Programme, plus sociodemographic characteristics, were obtained before screening (n = 628), 10 months (n = 93) and 2 years after screening started (n = 206). While knowledge about risk did not change, significant increases were found in the proportion of women who had heard of mammography, screening mammography specifically and the screening van. In addition there were significant increases in the proportion of women exposed to information about screening mammograms. The campaign generally had an equal effect on different sociodemographic but managed to achieve greater effects in women of non-English-speaking backgrounds and lower occupational status. A random sample of program attenders aged 45 to 70 (n = 763) were asked how they found out about the van. 'Seeing the van' was the most consistently reported source of awareness. Others included 'GPs' 'newspapers', 'other print media' and 'personal networks'. Women with additional qualifications since leaving school were more likely to state 'newspaper' and 'other print media' as a source.

Aged↗

Modeling and implementing a health information provider on the Internet.

OBJECTIVES: To model and implement a medical web portal providing access to well qualified and high-quality information. MATERIAL AND METHODS: The Unified Medical Language System (UMLS) knowledge sources of the U.S. National Library of Medicine and an Information Sources Catalog (ISC) resulting from the ARIANE project are described. The XML technology that allows files transformations by the means of XSLT is briefly presented. RESULTS: The design and implementation of software modules that exploit knowledge sources, operate the translation of a user's query to selected information sources, and wrap obtained results are detailed. DISCUSSION: Current implementation and wrapping perspectives are discussed in terms of integration and interoperability of health information resources.

Humans↗

Designing and implementing health data and information providers.

OBJECTIVES: To model and implement web portals providing access to certified and high-quality information in the domain of health. MATERIAL AND METHODS: The Unified Medical Language System (UMLS) knowledge sources of the U.S. National Library of Medicine and principles of implementation resulting from the previous ARIANE project are described. The XML technology that allows files transformations by the means of XSLT is briefly presented. RESULTS: The design and implementation of software modules that exploit knowledge sources, operate the translation of a user's query to selected information sources, and wrap obtained results are detailed. Querying documentary and factual medical databases are presented. DISCUSSION: Current implementation and wrapping perspectives are discussed in terms of integration and interoperability of health information and data resources.

France↗

An overview of statistical methods for the classification and retrieval of patient events.

Statistical methods that can support text retrieval are becoming an increasing focus of medical informatics activities. We overview our adaptation of existing knowledge sources to create pseudo-documents for concept based latent semantic indexing. Experience demonstrated this tack of limited practical value, since retrieval performance was invariably unsatisfactory. We discovered this was due in part to the introduction of a vocabulary gap between the queries and the cases we sought to retrieve. In part to address this problem, and to avail our large body of humanly coded text as a knowledge source, we developed a least squares fit alternative for the computer assisted indexing and retrieval of biomedical texts. This technique demonstrates equivalent or superior retrieval performance when compared to all other textual retrieval techniques. It does not depend upon elaborate knowledge bases, lexicons, or thesauri. It is a promising technique for classifying and retrieving the large volumes of clinical text.

Abstracting and Indexing↗

UMLS language and vocabulary tools.

A variety of resources developed for use with the Unified Medical Language System are presented. These resources include the UMLS Knowledge Source Server, the SPECIALIST lexicon, a set of lexical tools that work with the SPECIALIST lexicon, and a variety of other NLP document processing tools. These tools manage lexical variation, tokenize and parse text strings, suggest spelling variants, and provide text-to-concept mapping capabilities. The UMLS Knowledge Source Server is available under a license agreement. The other tools are freely downloadable.

Abstracting and Indexing↗

Safe asleep? Human-machine relations in medical practice.

In the process of anaesthesia the patient must surrender vital functions to the care of clinicians and machines who will act for, and advocate for the patient during the surgical procedure. In this paper, we discuss the practices and knowledge sources that underpin safety in a risky field in which many boundaries are crossed and dissolved. Anaesthetic practice is at the frontier not only of conscious/unconsciousness but is also at the human/machine frontier, where a range of technologies acts as both delegates and intermediaries between patient and practitioner. We are concerned with how practitioners accommodate and manage these shifting boundaries and what kinds of knowledge sources the 'expert' must employ to make decisions. Such sources include clinical, social and electronic which in their various forms demonstrate the hybrid and collective nature of anaesthetised patients. In managing this collective, the expert is one who is able to judge where the boundary lies between what is routine and what is critical in practice, while the junior must judge the personal limits of expertise in practice. In exploring the working of anaesthetic hybrids, we argue that recognising the changing distribution of agency between humans and machines itself illustrates important features of human authorship and expertise.

Anesthesiology↗

The Unified Medical Language System: an informatics research collaboration.

In 1986, the National Library of Medicine (NLM) assembled a large multidisciplinary, multisite team to work on the Unified Medical Language System (UMLS), a collaborative research project aimed at reducing fundamental barriers to the application of computers to medicine. Beyond its tangible products, the UMLS Knowledge Sources, and its influence on the field of informatics, the UMLS project is an interesting case study in collaborative research and development. It illustrates the strengths and challenges of substantive collaboration among widely distributed research groups. Over the past decade, advances in computing and communications have minimized the technical difficulties associated with UMLS collaboration and also facilitated the development, dissemination, and use of the UMLS Knowledge Sources. The spread of the World Wide Web has increased the visibility of the information access problems caused by multiple vocabularies and many information sources which are the focus of UMLS work. The time is propitious for building on UMLS accomplishments and making more progress on the informatics research issues first highlighted by the UMLS project more than 10 years ago.

Computer Communication Networks↗

[A study on the factors affecting friendship with HIV-infected students in high school: from the survey of AIDS related knowledge, information sources and attitudes in 1989 and 1992].

To clarify the factors affecting the friendship with human immunodeficiency virus (HIV)-infected persons, a self-reported questionnaire study was conducted in two high schools in Tokyo in 1989 and 1992. A complete set of responses was obtained from 541 (98%) and 517 (99%) students in 1989 and 1992, respectively. The following results were obtained: 1) The proportion of the students who received information on HIV/acquired immunodeficiency syndrome (AIDS) from school teachers in 1992 was higher than that in 1989 for both males and females. Similarly, for both males and females, the proportion of students with correct knowledge on HIV transmission was significantly higher in 1992. The proportion of the students who intended to have a friendship with a hypothetical HIV-infected classmate or close friend in 1992 was significantly higher. 2) The results of multiple logistic regression analysis indicated that such factors as having more correct knowledge on HIV transmission and considering the confidentiality of persons with HIV/AIDS were significantly related to having friendship with a hypothetical HIV-infected classmate for both 1989 and 1992; such factors as being a female and having an increasing risk of HIV infection were significantly related to the responses obtained for 1992.

Acquired Immunodeficiency Syndrome↗

An automated approach to studying health resource and infobutton use.

Many studies have found that clinicians require access to medical knowledge sources while viewing data in their patients' health records. To address this need, we have been developing links to various on-line health information resources from our Web-based clinical information system (WebCIS). Clinicians can access these resources through a "Health Resources" Web page or use context-sensitive "infobuttons" that automatically link to specific resources. To assist in understanding how clinicians interact with these two mechanisms, we have been exploring the use of an automated approach to answer questions about usage for guiding the further development of links to resources. In this paper, we discuss the use of a knowledge discovery technique (CIS Usage Mining) to obtain usage statistics from log files that record interactions with health resources and infobuttons in WebCIS, describe a Web-based interface developed to present the results, and summarize how the results could be applied. The availability of effective links to on-line medical knowledge sources from the patient health record can assist in resolving information needs, potentially improving patient care and decision-making.

Access to Information↗

Data-source effects on the sensitivities and specificities of clinical features in the diagnosis of rheumatoid arthritis: the relevance of multiple sources of knowledge for a decision-support system.

An experimental computer system was developed to support diagnosis of rheumatic disorders by computing diagnostic probabilities using modified likelihood ratios. The authors examined whether the performance of the model was affected by the settings in which the data used to derive the likelihood ratios were collected. The sensitivities and specificities of various clinical features for diagnosing rheumatoid arthritis (RA) were obtained from: 1) a study of 1,570 consecutive outpatients at a rheumatology clinic; 2) a review of the literature; 3) estimates by rheumatologists; and 4) a population study. Considerable variations in sensitivity and specificity but satisfactory agreement in likelihood ratios were found across the four data sets. The likelihood ratios were then used to compute the probabilities of RA in a test series of 570 of the rheumatology clinic outpatients. The model's diagnoses with likelihood ratios from the other sources were adequate. When the likelihood ratios from these sources were combined, discrimination came close to what could be achieved by using the likelihood ratios based on the data from the clinic. The method applied in the study, which makes use of variation of input data instead of variation of test series, and the results are relevant to assessing the external validity and transferability of Bayesian decision-support systems.

Adolescent↗