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Linking biomedical language information and knowledge resources: GO and UMLS.

Integration of various informatics terminologies will be an essential activity towards supporting the advancement of both the biomedical and clinical sciences. The GO consortium has developed an impressive collection of biomedical terms specific to genes and proteins in a variety of organisms. The UMLS is a composite collection of various medical terminologies, pioneered by the National Library of Medicine. In the present study, we examine a variety of techniques for mapping terms from one terminology (GO) to another (UMLS), and describe their respective performances for a small, curated data set attained from the National Cancer Institute, which had precision values ranging from 30% (100% recall) to 95% (74% recall). Based on each technique's performance, we comment on how each can be used to enrich an existing terminology (UMLS) in future studies and how linking biological terminologies to UMLS differs from linking medical terminologies.

Algorithms↗

Reaching and teaching new medical students.

OBJECTIVE: Each year 150 new medical students enter UCLA. During Foundations week they are introduced to the resources and services, which will support their studies, as well as to the problem-based learning (PBL) approach of instruction. The library is responsible for introducing print and digital resources and illustrating how these support the PBL approach. This has been a challenge, given students' belief that they already know about libraries and the limited time frame (roughly 45 minutes) allotted to us. This year we developed a collaborative, student-centered, active learning approach. Students were exposed to a variety of relevant resources and given the opportunity to critique them for appropriateness to their PBL case of the week. DESCRIPTION: Sessions were designed for 50 students at once in the instructional microcomputing facility (IMF), with two or three students sharing each workstation. Since the IMF is equipped with classroom control software, librarians could display resources on each workstation while discussing them. Since we wish to encourage students to begin at our Web page, we wore t-shirts with the logo "Start@Biomed" and our URL. Instruction started with a "Guided Tour of the Biomedical Library Web Page" during which we discussed general services, highlighted special features, including Web-based tutorials and subject guides, and illustrated how to connect to relevant resources such as PubMed, MDConsult, STAT!Ref, and MEDLINEPlus. The student groups then critically reviewed one resource identified by a card next to their workstation by answering the following questions in writing: Would this resource address your specific PBL learning issue? If not, what type of learning issue would it address? Describe an outstanding feature or a barrier to use for this resource? After ten minutes, students were asked to report to the entire group. The use of a hand-held mike, which we passed among the students, added an element of fun to the proceedings and simulated a talk show atmosphere. DISCUSSION: This emphasis on active learning, critical thinking, and problem solving was a successful way to introduce students to the library and its resources, and reinforced the library's role in PBL. The friendly, casual talk-show approach, coupled with our Start@Biomed t-shirts, created a setting in which we became real partners in the learning enterprise. Students reported they enjoyed the experience, and they are returning to us for additional help. Their written feedback, which we collected, summarized, and distributed to the entire class, illustrated a clear understanding of the resources and their usefulness. Both the medical school faculty and the librarians involved feel we have developed a useful, interesting, and appropriate way to reach beginning medical students, who often feel that they already know a great deal about using a library.

California↗

Generation of chicken Z-chromosome painting probes by microdissection for screening large-insert genomic libraries.

A strategy for rapid generation of chicken sex chromosome-Z painting probes has been developed using microdissection. Whole chromosome painting probes (WCPs) were prepared from 10-15 copies of mitotic metaphase chicken Z chromosomes. The microisolated chromosomes were subjected to PEG/proteinase K treatment in a collection drop to release DNA, which was then amplified using a degenerate oligonucleotide-primed shuttle PCR (DOP-Shuttle-PCR) strategy. Size distributions of the PCR products were analyzed by agarose gel electrophoresis and smears of DNA were revealed that ranged in size from 200-800 bp, without any evidence of preferential amplification. Both specificity and complexity of the probes have been analyzed by Southern blot and fluorescence in situ hybridization (FISH). Non-specific hybridization was efficiently blocked by using chicken competitor DNA. Analysis of the WCPs produced shows that collectively they provide uniform hybridization signals along the entire length of the chicken Z chromosome. To demonstrate one possible application of these complex probes, we screened a large-insert bacterial artificial chromosome (BAC) chicken genomic library to select Z chromosome-specific clones. To address specificity of the selected clones and to physically map them to the Z chromosome, FISH analysis was used. Of the 3 clones initially tested, one clone (C3) carrying a 250-kb insert mapped to the distal portion of the short arm of the chicken Z chromosome. Therefore, this technique has provided appropriate probes for screening large-insert genomic libraries. Further application of these probes includes the analysis of chromosome rearrangements, studies of cases of heteroploidy involving the Z chromosome, positional cloning of Z-linked genes and studies on mechanisms of sex-chromosome evolution in birds.

Animals↗

Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.

By mining publicly accessible databases, we have developed a collection of tissue-specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.

Databases, Protein↗

The telemedicine information exchange: an online resource.

Telemedicine is the use of telecommunications to provide health care services at a distance. It has grown from mostly government-subsidized research initiatives into a fledgling industry. This growth was fueled by decreasing costs of telecommunications and information technologies and fanned by rising health care costs. The telemedicine information exchange (TIE) (http:(/)/tie.telemed.org), developed by the Telemedicine Research Center in Portland, OR, is both a product and a vehicle of this rapid growth. It facilitates collection of telemedicine information from many sources, providing an easy-to-use hypertext format. This article describes the TIE's development, advantages and disadvantages of a web-based online library, and it's codevelopment with a rapidly expanding industry.

Costs and Cost Analysis↗

Using focus groups to discover health professionals' information needs: a regional marketing study.

This paper describes the use of focus groups as a data-gathering tool, in both theoretical and practical terms. Calder's discussion of focus groups is presented as the basis of the theory, and the marketing study conducted by the Midcontinental Region of the National Network of Libraries of Medicine serves as the backdrop to highlight some of the practical aspects of using this qualitative data-gathering method. Results of the marketing study are presented to illustrate the types of data that can be gathered using this methodology and the types of plans for future activities that can be developed based on the data gathered.

Communication↗

International exchange of scientific literature by U.S. academic health sciences libraries: a literature review and survey of current activities.

This paper reports results of a literature review and survey of current international exchange activities in 124 academic health sciences libraries in the United States. It describes the extent to which those libraries engage in exchange programs, the kinds of material sent and received, and the common problems in establishing and maintaining exchange relationships. Preferences of the respondents for future exchange programs are identified and recommendations for enhancing their value are made. The work reported is being used by the Medical Library Association Ad Hoc Committee on the International Exchange and Redistribution of Library Materials to develop a more workable and effective mechanism for continuing the international exchange of scientific literature and for facilitating the dissemination of scientific information to national and international network users.

Academic Medical Centers↗

[IMAGE: molecular integration of the analysis of the human genome and its expression].

We have developed an integrated approach for the analysis of human cDNA libraries from neuromuscular tissues, based on the acquisition of primary structural, expression and mapping data. 26,938 sequence signatures (over 7 million bases) have been derived from both ends of skeletal muscle and brain cDNA clones. Primary redundancy analysis and classification of database similarities made it possible to characterize by structural data about 8,000 human gene transcripts, the majority of which is catalogued for the first time. Collecting hybridization signatures of complex cDNA probes derived from the tissues of origin to cDNA clones arrayed on high density filters provided a global and quantifiable view of the complexity and level of expression of the different transcripts. The development of 2,792 eSTS markers amplifiable by PCR defined the chromosomal localization of some 2,500 genes corresponding to the transcripts sequenced. The data collected are part of the corpus of the human gene transcript catalog and the genic map of the human genome.

Brain Chemistry↗

The patient-centered bibliography: uniting library services with the mission of the psychiatric hospital.

The primary function of a hospital is patient care. The development of a patient-centered bibliography is suggested as the most effective way of organizing information and insuring its use in the psychiatric hospital. The patient-centered bibliography is a collection of readings which are especially pertinent to the care of an individual patient. It consists of a core of current literature organized around the patient's multiaxial diagnosis (including psychosocial stresses), but may also include articles on psychopharmacology, special psychotherapeutic techniques, and literature on family dynamics. The collection can be expanded to include patient-centered information for two other purposes as well: milieu therapy and patient education.

Bibliographies as Topic↗

Derivatization procedures for gas chromatographic-mass spectrometric determination of xenobiotics in biological samples, with special attention to drugs of abuse and doping agents.

The development of low cost MS detectors in recent years has promoted an important increase in the applicability of GC-MS system to analyze for the presence of foreign substances in the human body. Drugs and toxic agents are in vivo metabolized in such a way that more polar compounds are usually formed. Derivatization of these metabolites is often an unavoidable requirement for gas chromatographic analysis. Application of derivatization methods in recent years has been relevant, especially for silylation, acylation, alkylation and the formation of cyclic or diastereomeric derivatives. Given the relevance of drug of abuse testing in modern toxicology, main derivatization procedures for opiates, cocaine, cannabis, amphetamines, benzodiazepines and LSD have been reviewed. Papers describing the analyses of drugs of abuse in matrixes other than blood, such as hair or sweat, have received special attention. Advances in derivatization for sports drug testing have been particularly relevant for anabolic steroids, diuretics and corticosteroids. Among the several methodologies applied, the formation of trimethylsilyl, perfluoroacyl or methylated derivatives have proved to be both versatile and extensively used. Further advances in derivatization for GC-MS applications in clinical and forensic toxicology will depend on the one hand on the degree of further use of GC-MS for routine applications and, on the other hand, on the alternative progress made for developments in LC-MS or CE-MS. Last but not least, the appearance of comprehensive libraries in which reference spectra for different derivatives of many drugs and their metabolites are collected will have an important impact on the expansion of derivatization in GC-MS for toxicological applications.

Body Fluids↗

Analysis of libraries encoded with GC tags: compound elution, tag decode analysis, and statistical sampling analysis.

Libraries encoded with electrophoric tags present a unique challenge with respect to library quality control and characterization. Libraries are prepared on Tentagel resin in 200-fold redundancy wherein each resin particle contains one compound per one tag set. The amount of compound present on the bead is ca. 200-500 pmole while tag levels are estimated at 0.5-1 pmol/bead. Several quality control protocols have been developed in order to accurately estimate bead yield and purity for the entire library, ensure high tag fidelity, and to determine the overall performance of individual synthons. This review provides a unique, collective portrait of Pharmacopeia's approach in assessing the quality of libraries prepared using its molecular encoding technology.

Chromatography, Liquid↗

Appropriate information: new products and services.

Effective health information services require action on three major levels: identifying and acquiring appropriate resources; applying appropriate methodologies for management of information and its communication; and stimulating local initiatives and applications. WHO's Programme of Library and Health Literature Services proposes its methodologies and products for creating and improving effective information services to health workers.

Developing Countries↗

Structured data management--the design and implementation of a web-based video archive prototype.

In response to the lack of readily available multimedia rich medical knowledge sources to support medical education and patient care, we designed and implemented a web-based video publishing platform. In order to promote the development of high-quality, up-to-date educational content, we have devised a scalable structure that allows online submissions and continuous updating of video and accompanying textual descriptions. Our goal is to enable experts in varied medical domains to collaborate in the construction of a video library using an intuitive web-based interface. Neurologists at Stanford built a well-annotated neurology video collection that initially emphasized childhood and adult movement disorders. The collection may be accessed either as a stand-alone resource or as part of the Stanford Skolar MD, an integrated online medical knowledge provider. This manuscript discusses the design framework and implementation details of structured media content development. We present examples illustrating media data collection, content indexing using UMLS concepts, media storage, and web presentation.

Abstracting and Indexing↗

Improving usage of pediatric information on the Internet: the Virtual Children's Hospital.

OBJECTIVE: Digital health sciences libraries (DHSLs) bring order to the chaos of the Internet by making authoritative medical information easily and conveniently available to patrons. The goal of this project was to perform a baseline usage analysis of the pediatric-related information in a general DHSL and to determine whether reorganization of the pediatric-related information into its own pediatric DHSL could increase the usage of the pediatric-related information. METHODS: From March through August 1997, a baseline analysis of a general DHSL (Virtual Hospital) was conducted using computer server log file analysis programs. The quantity of pediatric-related information in the general DHSL and its baseline usage were determined. In September 1997, the pediatric-related information was reorganized into its own pediatric DHSL (Virtual Children's Hospital), and server log file analyses were conducted of the pediatric DHSL from September 1997 to August 1998. Statistical analysis was performed by time series autoregression. RESULTS: During the baseline, the general DHSL and the pediatric-related information received a monthly average of 2 320 782 and 141 444 qualified hits, respectively. After the intervention, the general DHSL and the pediatric DHSL received a monthly average of 2 765 454 and 256 998 qualified hits, respectively. This is an increase of 19. 2% for the general DHSL and 81.7% for the pediatric DHSL. These changes were statistically significant at the P >.0001 level. The most requested pediatric-related content in the pediatric DHSL did not change substantively from preintervention to postintervention. DISCUSSION: On the Internet, as in real life, children's services must have their own distinct identity and must be differentiated from adult services. Therefore, pediatric-related information will receive increased usage if it is part of a pediatric DHSL rather than part of a general DHSL. Others can use this process and the lessons learned to develop and enhance their own pediatric-related information on the Internet. Internet, pediatrics, digital health sciences libraries, digital library, medical library.

Data Collection↗

Using the Internet as a teaching strategy: informatics at work.

Development of the World Wide provides educators with an enormous library of teaching tools. The purpose of this presentation is to share the results of introducing over 60 graduate students to use e-mail, internet mailing lists, computer conferences, and the World Wide Web as teaching strategies. Data were collected from students through questions and Electronic Communication Logs. Response of the students was categorized into 6 phases: 1) fear and trepidation, 2) excitement, "this is great!", 3) "help, my mail box is full", 4) venturing forth independently, 5) this is easy, and 6) accepting the internet as a useful tool. Identification of these phases provided a basis for developing teaching strategies specific to internet uses. Feedback between students and instructor increased and was far more timely than occurs in the classroom setting. The student responses to these experiences were overwhelmingly positive.

Computer Communication Networks↗

A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.

MOTIVATION: Massive oligonucleotide hybridization is one of the most promising technologies of functional genome analysis. The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization. RESULTS: Using a genetic algorithm approach, we have attempted to design sets of oligo probes capable of identifying new genes belonging to a defined gene family within a cDNA or genomic library. It is not limited by oligonucleotide length and admits the letter 'N' in the structure of the oligonucleotides selected. One of the major advantages of this approach is the low homology required to identify functional families of sequences with little homology. We have designed the oligonucleotide sets that are most selective for the cDNA clones of transmembrane G protein-coupled receptors (GPCRs), a large family of proteins that form part of a modular system of extracellular signal transduction to the intracellular second messenger pathways. The accuracy of identification has been checked on the EST library containing 713 870 cDNA sequences. A set of 15 oligos between 7 and 14 bases in length has correctly identified 70% of the GPCR cDNA collection sequences with 0.02% false positives. AVAILABILITY: The developed software is available by ftp://ftp.bionet.nsc. ru/pub/biology/ and on the Web page http://www.bionet.nsc. ru/SRCG/Oligoselector/. CONTACT: kel@.bionet.nsc.ru; sebastian. meier-ewert@gpc-ag.com

Algorithms↗

An ordered collection of expressed sequences from Cryphonectria parasitica and evidence of genomic microsynteny with Neurospora crassa and Magnaporthe grisea.

Cryphonectria parasitica, the causative agent of chestnut blight, has proven to be a tractable experimental system for studying fungal pathogenesis. Moreover, the development of infectious cDNA clones of C. parasitica hypoviruses, capable of attenuating fungal virulence, has provided the opportunity to examine molecular aspects of fungal plant pathogenesis in the context of biological control. In order to establish a genomic base for future studies of C. parasitica, the authors have analysed a collection of expressed sequences. A mixed cDNA library was prepared from RNA isolated from wild-type (virus-free) and hypovirus-infected C. parasitica strains. Plasmid DNA was recovered from individual transformants and sequenced from the 5' end of the insert. Contig analysis of the collected sequences revealed that they represented approximately 2200 individual ORFs. An assessment of functional diversity present in this collection was achieved by using the BLAST software utilities and the NCBI protein database. Candidate genes were identified with significant potential relevance to C. parasitica growth, development, pathogenesis and vegetative incompatibility. Additional investigations of a 12.9 kbp genomic region revealed microsynteny between C. parasitica and both Neurospora crassa and Magnaporthe grisea, two closely related fungi. These data represent the largest collection of sequence information currently available for C. parasitica and are now forming the basis of further studies using microarray analyses to determine global changes in transcription that occur in response to hypovirus infection.

Amino Acid Sequence↗

The Association of Academic Health Sciences Libraries Annual Statistics: an exploratory twenty-five-year trend analysis.

This paper presents an exploratory trend analysis of the statistics published over the past twenty-four editions of the Annual Statistics of Medical School Libraries in the United States and Canada. The analysis focuses on the small subset of nineteen consistently collected data variables (out of 656 variables collected during the history of the survey) to provide a general picture of the growth and changing dimensions of services and resources provided by academic health sciences libraries over those two and one-half decades. The paper also analyzes survey response patterns for U.S. and Canadian medical school libraries, as well as osteopathic medical school libraries surveyed since 1987. The trends show steady, but not dramatic, increases in annual means for total volumes collected, expenditures for staff, collections and other operating costs, personnel numbers and salaries, interlibrary lending and borrowing, reference questions, and service hours. However, when controlled for inflation, most categories of expenditure have just managed to stay level. The exceptions have been expenditures for staff development and travel and for collections, which have both outpaced inflation. The fill rate for interlibrary lending requests has remained steady at about 75%, but the mean ratio of items lent to items borrowed has decreased by nearly 50%.

Annual Reports as Topic↗