Genomes and Genes
Summary: Extensive collections, reputedly complete, of references and citations to books, articles, publications, etc., generally on a single subject or specialized subject area. Databases can operate through automated files, libraries, or computer disks. The concept should be differentiated from DATABASES, FACTUAL which is used for collections of data and facts apart from bibliographic references to them.
Publications200 found, 100 shown here
- 404 not found: the stability and persistence of URLs published in MEDLINEJonathan D Wren
Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
Bioinformatics 20:668-72. 2004..An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal...
- Recognizing names in biomedical texts: a machine learning approachGuodong Zhou
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
Bioinformatics 20:1178-90. 2004..In order to make organized and structured information available, automatically recognizing biomedical entity names becomes critical and is important for information retrieval, information extraction and automated knowledge acquisition...
- Should meta-analysts search Embase in addition to Medline?Margaret Sampson
Chalmers Research Group, Children s Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
J Clin Epidemiol 56:943-55. 2003..88-0.99). Searching Medline but not Embase risks biasing a meta-analysis by finding studies that show larger estimates, but their prevalence seems low enough that the risk may be slight, provided the rest of the search is comprehensive...
- ABNER: an open source tool for automatically tagging genes, proteins and other entity names in textBurr Settles
Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin Madison Madison, WI 52706, USA
Bioinformatics 21:3191-2. 2005..It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora...
- Five large Chinese biomedical bibliographic databases: accessibility and coverageJun Xia
Cochrane Schizophrenia Group, University of Nottingham, Nottingham, UK
Health Info Libr J 25:55-61. 2008..Much biomedical research is now undertaken in China...
- Google Scholar: A source for clinicians?Jim Henderson
Health Sciences Library, McGill University, Montreal, Que
CMAJ 172:1549-50. 2005
- Searching for the right search--reaching the medical literatureRobert Steinbrook
N Engl J Med 354:4-7. 2006
- Literature searching for randomized controlled trials used in Cochrane reviews: rapid versus exhaustive searchesPamela Royle
Wessex Institute for Health Research and Development
Int J Technol Assess Health Care 19:591-603. 2003..To analyze sources searched in Cochrane reviews, to determine the proportion of trials included in reviews that are indexed in major databases, and to compare the quality of these trials with those from other sources...
- Developing optimal search strategies for detecting clinically sound and relevant causation studies in EMBASER Brian Haynes
Health Information Research Unit, Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
BMC Med Inform Decis Mak 5:8. 2005..Although such filters have previously been developed for studies of relevance to causation in MEDLINE, no empirically tested search strategy exists for EMBASE...
- Comparing test searches in PubMed and Google ScholarMary Shultz
Library of the Health Sciences Urbana, University of Illinois at Chicago, 102 Medical Sciences Building, 506 South Mathews Avenue, Urbana, IL 61801, USA
J Med Libr Assoc 95:442-5. 2007
- SGD: Saccharomyces Genome DatabaseJ M Cherry
Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
Nucleic Acids Res 26:73-9. 1998..SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/..
- Unique author identification number in scientific databases: a suggestionMatthew E Falagas
PLoS Med 3:e249. 2006
- Database searches for qualitative researchDavid Evans
The Joanna Briggs Institute for Evidence Based Nursing and Midwifery and University of Adelaide, South Australia, Australia
J Med Libr Assoc 90:290-3. 2002..These difficulties relate to the descriptive nature of the titles used in some qualitative studies, the variable information provided in abstracts, and the differences in the indexing of these studies across databases...
- Do the findings of case series studies vary significantly according to methodological characteristics?K Dalziel
Peninsula Technology Assessment Group, Peninsula Medical School, Universities of Exeter and Plymouth, Exeter, UK
Health Technol Assess 9:iii-iv, 1-146. 2005....
- Coverage of the bibliographic databases in mental health researchJohanna Löhönen
Department of Psychiatry, University of Oulu, PO Box 5000, 90014 Oulun yliopisto, Finland
Nord J Psychiatry 64:181-8. 2010Electronic bibliographic databases are important tools when searching for medical information. The selected databases have an important effect on the potential results achieved...
- Accomplishments and challenges in literature data mining for biologyLynette Hirschman
The MITRE Corporation, USA
Bioinformatics 18:1553-61. 2002..To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context...
- Textpresso: an ontology-based information retrieval and extraction system for biological literatureHans Michael Muller
Division of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
PLoS Biol 2:e309. 2004..Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org...
- Show me the dataMike Rossner
J Cell Biol 179:1091-2. 2007
- A guide for medical information searches of bibliographic databases - psychiatric research as an exampleJohanna Löhönen
Department of Psychiatry, University of Oulu, Oulu, Finland
Int J Circumpolar Health 68:394-404. 2009Information overload, demanding work with strict time limits, and the extensive number of medical bibliographic databases and other research sources all underline the importance of being able to search for up-to-date information ..
- Identifying diagnostic accuracy studies in EMBASELucas M Bachmann
Horten Centre, Bolleystrasse 40, Postfach Nord, University of Zurich, CH 8091 Zurich, Switzerland
J Med Libr Assoc 91:341-6. 2003..The objective was to develop and test search strategies to identify diagnostic articles recorded on EMBASE...
- Extracting synonymous gene and protein terms from biological literatureHong Yu
Department of Computer Science, Columbia University, New York, NY, USA
Bioinformatics 19:i340-9. 2003..Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance...
- How important are comprehensive literature searches and the assessment of trial quality in systematic reviews? Empirical studyM Egger
Department of Social and Preventive Medicine, University of Berne, Switzerland
Health Technol Assess 7:1-76. 2003
- Developing optimal search strategies for detecting clinically sound treatment studies in EMBASESharon S L Wong
School of Nutrition Faculty of Community Services Ryerson University Toronto, Ontario M5B 2K3 Canada
J Med Libr Assoc 94:41-7. 2006The ability to accurately identify articles about therapy in large bibliographic databases such as EMBASE is important for researchers and clinicians...
- Developing efficient search strategies to identify reports of adverse effects in MEDLINE and EMBASESu Golder
Centre for Reviews and Dissemination, University of York, UK
Health Info Libr J 23:3-12. 2006..This study aimed to assess the performance, in terms of sensitivity and precision, of different approaches to searching MEDLINE and EMBASE to identify studies of adverse effects...
- Analysis of genomic and proteomic data using advanced literature miningYanhui Hu
Institute of Proteomics, Harvard Medical School BCMP, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
J Proteome Res 2:405-12. 2003..Interestingly, this only held true for estrogen receptor (ER) positive tumors, not ER negative. MedGene identified a set of relatively understudied, yet highly expressed genes in ER negative tumors worthy of further examination...
- Tools for loading MEDLINE into a local relational databaseDiane E Oliver
Department of Genetics, Stanford University, Stanford, CA, USA
BMC Bioinformatics 5:146. 2004..Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers...
- Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptorsFlorence Horn
Department of Cellular and Molecular Pharmacology, University of California of San Francisco, 94143, USA
Bioinformatics 20:557-68. 2004..The main aim of the MCSIS project is to gather heterogeneous data from across a variety of electronic and literature sources in order to draw new inferences about the target protein families...
- Evolution of medical informatics in bibliographic databasesPaula Otero
Department of Medical Informatics, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
Stud Health Technol Inform 107:301-5. 2004..We compared the presentation of Medical Informatics in two different bibliographic databases: MEDLINE and LILACS (Latin American and Caribbean Literature on the Health Sciences)...
- The handsearching of 2 medical journals of Bahrain for reports of randomized controlled trialsAmani A Al-Hajeri
Genetic Department, Salmaniyah Medical Complex, Kingdom of Bahrain
Saudi Med J 27:526-30. 2006....
- [Evaluation of two methods for correcting the impact factor using the investigation done at the "Del Río Hortega" University Hospital (1999-2004) as the data source]M González-Sagrado
Unidad de Apoyo a la Investigación, Hospital Universitario del Rio Hortega, Valladolid, Spain
Nutr Hosp 23:111-8. 2008..Our objective was to evaluate two parameters (the maximum and the median value of each subject area) for IF adjustment using the original (not corrected) IF as the reference method in a tertiary hospital biomedical investigation model...
- Clinical Evidence diagnosis: Developing a sensitive search strategy to retrieve diagnostic studies on deep vein thrombosis: a pragmatic approachSam Vincent
Clinical Evidence, London, UK
Health Info Libr J 20:150-9. 2003..To devise and evaluate a sensitive search strategy to retrieve diagnostic studies on specific diagnostic tests for deep vein thrombosis (DVT)...
- Twenty years of health care economic analysis in Spain: are we doing well?A Garcia-Altes
Catalan Agency for Health Technology Assessment and Research, Fundación Instituto de Investigación en Servicios de Salud, Spain
Health Econ 10:715-29. 2001....
- Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomideMarc Weeber
Department of Social Pharmacy and Pharmacoepidemiology, Groningen University Institute for Drug Exploration, The Netherlands
J Am Med Inform Assoc 10:252-9. 2003..However, experimental and clinical evaluation is needed to validate these hypotheses and to assess the trade-off between therapeutic benefits and toxicities...
- EMBASE search strategies for identifying methodologically sound diagnostic studies for use by clinicians and researchersNancy L Wilczynski
Health Information Research Unit, Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, L8N 3Z5 Canada
BMC Med 3:7. 2005..b>Bibliographic databases such as EMBASE provide the most widely available entrée to this literature...
- PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literatureG R Grimes
The Scottish Centre for Genomic Technology and Informatics, University of Edinburgh 49 Little France Crescent, Edinburgh EH16 4SB, UK
Bioinformatics 22:2055-7. 2006..PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research...
- MutationFinder: a high-performance system for extracting point mutation mentions from textJ Gregory Caporaso
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA
Bioinformatics 23:1862-5. 2007..We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline...
- Public health. Increasing international gaps in health-related publicationsGuillermo Paraje
World Health Organization CH 1211 Geneva 27 Switzerland
Science 308:959-60. 2005
- Knowledge discovery by automated identification and ranking of implicit relationshipsJonathan D Wren
Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
Bioinformatics 20:389-98. 2004....
- A literature network of human genes for high-throughput analysis of gene expressionT K Jenssen
Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway
Nat Genet 28:21-8. 2001..We validated the applicability of the tools by analyzing two publicly available microarray data sets...
- Searching the Literatura Latino Americana e do Caribe em Ciências da Saúde (LILACS) database improves systematic reviewsOtavio Augusto Camara Clark
Instituto do Radium, Campinas, Sao Paulo, Brazil
Int J Epidemiol 31:112-4. 2002..Our objective is to evaluate if LILACS should be used as a routine source of articles for SR...
- Evidence-based practice: extending the search to find material for the systematic reviewD Helmer
British Columbia Office of Health Technology Assessment, Centre for Health Services and Policy Research, University of British Columbia, Vancouver, Canada
Bull Med Libr Assoc 89:346-52. 2001..The quality of the items uncovered has yet to be assessed and will be key in evaluating the value of the systematic search methods...
- Searching for the evidence in pre-hospital care: a review of randomised controlled trials. On behalf of the Ambulance Response Time Sub-Group of the National Ambulance Advisory CommitteeH Brazier
The Library, Royal College of Surgeons in Ireland, Dublin 2
J Accid Emerg Med 16:18-23. 1999..To identify randomised controlled trials (RCTs) which evaluate aspects of pre-hospital care; to perform categorisation by theme; to compare the sensitivity and precision of the search databases...
- Word sense disambiguation in the biomedical domain: an overviewMartijn J Schuemie
Biosemantics Group, Medical Informatics Department, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
J Comput Biol 12:554-65. 2005..WSD algorithms should preferably be able to take into account both known and unknown senses of a word. Without WSD, automatic metaanalysis of large corpora of text will be error prone...
- Personalized online information search and visualizationDongquan Chen
Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
BMC Med Inform Decis Mak 5:6. 2005..The retrieved information will be available anytime and anywhere through a secure web server...
- Discovering patterns to extract protein-protein interactions from full textsMinlie Huang
State Key Laboratory of Intelligent Technology and Systems, Department of Computer Science and Technology, University of Tsinghua, Beijing, 100084, China
Bioinformatics 20:3604-12. 2004..Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein-protein interactions from biomedical texts...
- Show me the dataMike Rossner
J Exp Med 204:3052-3. 2007
- An overview of the design and methods for retrieving high-quality studies for clinical careNancy L Wilczynski
Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
BMC Med Inform Decis Mak 5:20. 2005With the information explosion, the retrieval of the best clinical evidence from large, general purpose, bibliographic databases such as MEDLINE can be difficult...
- World databases of summaries of articles in the biomedical fieldsMatthew E Falagas
Arch Intern Med 167:1204-6. 2007
- The modest but growing Brazilian presence in psychiatric, psychobiological and mental health research: assessment of the 1998-2002 periodR A Bressan
Departamento de Psiquiatria, Universidade Federal de Sao Paulo, Sao Paulo, SP, Brasil
Braz J Med Biol Res 38:649-59. 2005..Based on these data, it is reasonable to predict a tendency to an increase in production over the next few years...
- Resolving abbreviations to their senses in MedlineS Gaudan
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 21:3658-64. 2005..Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems...
- The European Network of Health Economic Evaluation Databases (EURO NHEED) ProjectJohn Nixon
Centre for Reviews and Dissemination, University of York, York YO10 5DD, UK
Eur J Health Econ 5:183-7. 2004..The project will therefore advance the state of the art in collecting, summarising, critiquing and disseminating economic evaluations of healthcare conducted within Europe...
- ADAM: another database of abbreviations in MEDLINEWei Zhou
Department of Psychiatry and Psychiatric Institute, MC912, University of Illinois at Chicago Chicago, IL 60612, USA
Bioinformatics 22:2813-8. 2006..We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations...
- Term identification in the biomedical literatureMichael Krauthammer
Department of Biomedical Informatics, Columbia Genome Center, Columbia University, New York, USA
J Biomed Inform 37:512-26. 2004..By assessing previous work in context of the overall term identification process, the review also tries to delineate needs for future work in the field...
- MILANO--custom annotation of microarray results using automatic literature searchesRan Rubinstein
Department of Molecular Biology, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
BMC Bioinformatics 6:12. 2005..Literature mining--the process of representing literature data in a fashion that is easy to relate to genomic data--is one solution to this problem...
- A survey of current work in biomedical text miningAaron M Cohen
Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, 3181 S W Sam Jackson Park Road, Portland, OR 97239 309, USA
Brief Bioinform 6:57-71. 2005....
- Using name-internal and contextual features to classify biological termsManabu Torii
Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, USA
J Biomed Inform 37:498-511. 2004..The experiments were conducted on the GENIA corpus Ver. 3.0 developed at University of Tokyo. We achieve f value of 86 in 10-fold cross validation evaluation on this corpus...
- Optimal search strategies for identifying sound clinical prediction studies in EMBASEJennifer L Holland
Department of Clinical Epidemiology and Biostatistics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
BMC Med Inform Decis Mak 5:11. 2005..We undertook the systematic development of search strategies ("hedges") for retrieval of empirically tested clinical prediction guides from EMBASE...
- The next generation of literature analysis: integration of genomic analysis into text miningMatthias Scherf
Genomatix Software GmbH, Landsberger Strasse 6, Munich, D 80339, Germany
Brief Bioinform 6:287-97. 2005....
- Searching bibliographic databases for literature on chronic disease and work participationJoke Haafkens
Academic Medical Centre, Coronel Institute, Amsterdam, The Netherlands
Occup Med (Lond) 56:39-45. 2006..Information on this topic is dispersed across a variety of data sources, making it difficult for health professionals to find relevant studies for literature reviews and guidelines...
- CoPub Mapper: mining MEDLINE based on search term co-publicationBlaise T F Alako
Department of Molecular Design and Informatics, Organon NV, P O Box 20, 5340 BH Oss, The Netherlands
BMC Bioinformatics 6:51. 2005..In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned...
- eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publicationsMounir Errami
McDermott Center for Human Growth and Development and the Department for Translational Research, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9185, USA
Nucleic Acids Res 35:W12-5. 2007..These services are freely accessible through the Internet at http://invention.swmed.edu/etblast/etblast.shtml, where users can upload a file or paste text such as an abstract into the browser interface...
- BioRAT: extracting biological information from full-length papersDavid P A Corney
Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
Bioinformatics 20:3206-13. 2004..BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE...
- Conservative treatment of acute and chronic nonspecific low back pain. A systematic review of randomized controlled trials of the most common interventionsM W van Tulder
Institute for Research in Extramural Medicine, Vrije Universiteit, Amsterdam, The Netherlands
Spine (Phila Pa 1976) 22:2128-56. 1997....
- Status of text-mining techniques applied to biomedical textRamón A A Erhardt
Bioalma, Ronda de Poniente 4, 28760 Tres Cantos, Madrid, Spain
Drug Discov Today 11:315-25. 2006..In the biomedical field, extracting information has specific problems: complex and ever-changing nomenclature (especially genes and proteins) and the limited representation of domain knowledge...
- GENIA corpus--semantically annotated corpus for bio-textminingJ D Kim
CREST, Japan Science and Technology Corporation, Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
Bioinformatics 19:i180-2. 2003..The lack of an extensively annotated corpus of this literature, however, causes a major bottleneck for applying NLP techniques. GENIA corpus is being developed to provide reference materials to let NLP techniques work for bio-textmining...
- Handsearching the EMHJ for reports of randomized controlled trials by U.K. Cochrane Centre (Bahrain)A Al Hajeri
Bahrain Branch of U K Cochrane Centre, The Cochrane Collaboration, Bahrain Correspondence to A Al
East Mediterr Health J 12:S253-7. 2006..Reports identified were sent to the UK Cochrane Centre for verification and publication in The Cochrane Central Register of Controlled Trials (CENTRAL)...
- Duplicate publication and 'paper inflation' in the Fractals literatureR N Kostoff
Office of Naval Research, 875 North Randolph Street, Arlington, VA 22217, USA
Sci Eng Ethics 12:543-54. 2006..This 'paper inflation' is due in large part to the increasing use of metrics (publications, patents, citations, etc) to evaluate research performance, and the researchers' motivation to maximize the metrics...
- The typical Cochrane review. How many trials? How many participants?Susan Mallett
Int J Technol Assess Health Care 18:820-3. 2002..To describe the number of trials and participants in a typical systematic review from The Cochrane Database of Systematic Reviews...
- PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search enginesThomas E Vanhecke
Department of Internal Medicine, William Beaumont Hospital, 3061 W 13 Mile Rd, Royal Oak, MI 48073, USA
Comput Biol Med 37:1252-8. 2007..PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines...
- Gene name identification and normalization using a model organism databaseAlexander A Morgan
MITRE Corporation, 202 Burlington Road, Mail Stop K325, Bedford, MA 01730 1420, USA
J Biomed Inform 37:396-410. 2004....
- Off-label use of medicines in children: can available evidence avoid useless paediatric trials? The case of proton pump inhibitors for the treatment of gastroesophageal reflux diseaseGiovanni Tafuri
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P O Box 80 082, 3508 TB, Utrecht, The Netherlands
Eur J Clin Pharmacol 65:209-16. 2009..In some cases of drug therapy, the available evidence might be sufficient to extend the indications to children without further clinical studies...
- PubNet: a flexible system for visualizing literature derived networksShawn M Douglas
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Genome Biol 6:R80. 2005..This feature allows one to, for example, examine a literature derived network of genes based on functional similarity...
- Lessons for search strategies from a systematic review, in The Cochrane Library, of nutritional supplementation trials in patients after hip fractureA Avenell
Health Services Research Unit, University of Aberdeen, Aberdeen, United Kingdom
Am J Clin Nutr 73:505-10. 2001..A key aim when conducting systematic reviews of randomized controlled trials (RCTs) is to include all of the evidence, if possible. Serious bias may result if trials are missed through inadequate search strategies...
- Identifying clinical trials in the medical literature with electronic databases: MEDLINE alone is not enoughM E Suarez-Almazor
Baylor College of Medicine, Houston, TX, USA
Control Clin Trials 21:476-87. 2000..Our findings suggest that the use of MEDLINE alone to identify CCTs is inadequate. The use of two or more databases and hand searching of selected journals are needed to perform a comprehensive search...
- Searching bibliographic databases effectivelyJ E Eyers
London School of Hygiene and Tropical Medicine, UK
Health Policy Plan 13:339-42. 1998The ability to search bibliographic databases effectively is now an essential skill for anyone undertaking research in health...
- Evaluation of methodological search filters--a reviewMichelle Jenkins
Department of Information and Communications, Manchester Metropolitan University, Manchester Royal Infirmary, UK
Health Info Libr J 21:148-63. 2004....
- Biomedical named entity recognition using two-phase model based on SVMsKi Joong Lee
Natural Language Processing Laboratory, Department of Computer Science and Engineering, Korea University, 1, 5 Ka, Anam Dong, Seoul 136 701, Republic of Korea
J Biomed Inform 37:436-47. 2004..The F-score (beta=1) for the boundary identification is 74.8 and the F-score for the semantic classification is 66.7...
- Discovering semantic features in the literature: a foundation for building functional associationsMonica Chagoyen
Biocomputing Unit, Centro Nacional de Biotecnologia CSIC, Madrid, Spain
BMC Bioinformatics 7:41. 2006..Therefore, the development of automated text mining tools to assist in such interpretation is one of the main challenges in current bioinformatics research...
- An entity tagger for recognizing acquired genomic variations in cancer literatureRyan T McDonald
Department of Computer and Information Science, University of Pennsylvania, 3330 Walnut Street, Philadelphia, PA 19104, USA
Bioinformatics 20:3249-51. 2004..VTag was tested with 345 training and 200 evaluation documents pertaining to cancer genetics. Our experiments resulted in 0.8541 precision, 0.7870 recall and 0.8192 F-measure on the evaluation set...
- Getting started in text miningK Bretonnel Cohen
University of Colorado School of Medicine, Center for Computational Pharmacology, UCHSC at Fitzsimons, Department of Pharmacology, Aurora, Colorado, United States of America
PLoS Comput Biol 4:e20. 2008
- Using statistical and knowledge-based approaches for literature-based discoveryMeliha Yetisgen-Yildiz
Information School, University of Washington, Seattle, WA, USA
J Biomed Inform 39:600-11. 2006..We also evaluate LitLinker's performance by using the information retrieval metrics of precision and recall...
- SaRAD: a Simple and Robust Abbreviation DictionaryEytan Adar
HP Laboratories, 1501 Page Mill Rd, Palo Alto, CA 94304, USA
Bioinformatics 20:527-33. 2004..Due to recent interest in the use of textual material to augment traditional experiments it has become necessary to automatically cluster, classify and filter natural language information...
- MedBlast: searching articles related to a biological sequenceQiang Tu
Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People s Republic of China
Bioinformatics 20:75-7. 2004..Here we developed a new literature-mining tool MedBlast, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided...
- Do clinicians use online evidence to support patient care? A study of 55,000 cliniciansJohanna I Westbrook
Centre for Health Informatics, Level 2, Samuels Building, University of New South Wales, Kensington, 2052, Australia
J Am Med Inform Assoc 11:113-20. 2004....
- The what and whys of DOIsSusanne DeRisi
PLoS Biol 1:E57. 2003
- Tough mining: the challenges of searching the scientific literatureSteven Dickman
PLoS Biol 1:E48. 2003
- Mapping the literature of health care managementMary K Taylor
Library Affairs, Southern Illinois University Carbondale, Morris Library, Carbondale, IL 62901, USA
J Med Libr Assoc 95:e58-65. 2007..The research provides an overview of the health care management literature and the indexing coverage of core journal literature...
- Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoidG D Zhou
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
Int J Med Inform 75:456-67. 2006..1 and V3.0, respectively. In particular, our system achieves an F-measure of 77.8 on the "protein" class of GENIA V3.0. It also shows that our system outperforms the best-reported system on GENIA V1.1 and V3.0...
- [Growth and trends in scientific production in epidemiology in Brazil]Mauricio L Barreto
Instituto De Saude Coletiva, Universidade Federal da Bahia, Salvador, BA, Brasil
Rev Saude Publica 40:79-85. 2006..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...
- Zone analysis in biology articles as a basis for information extractionYoko Mizuta
National Institute of Informatics, 2 1 2 Hitotsubashi, 101 8430 Tokyo, Japan
Int J Med Inform 75:468-87. 2006..We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework...
- [Presence of the biomedical periodicals of Hungarian editions in international databases]Lívia Vasas
Semmelweis Egyetem, Központi Könyvtár
Orv Hetil 147:73-81. 2006..of Hungarian interests were not represented with reasonable emphasis in the relevant international bibliographic databases. Because of the great number of data the scientific literature of medicine and related sciences could not ..
- Text mining and ontologies in biomedicine: making sense of raw textIrena Spasic
School of Chemistry, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK
Brief Bioinform 6:239-51. 2005..The principal link between text and an ontology is terminology, which maps terms to domain-specific concepts. This paper summarises different approaches in which ontologies have been used for text-mining applications in biomedicine...
- Journals in surgery and gastroenterology: indexing in databases and bibliometric indicatorsRegina C Figueiredo Castro
BIREME, PAHO, WHO, Sao Paulo, Brazil
Acta Cir Bras 21:122-32. 2006..To select where to publish, authors must know how to identify the most recognized journals in each field, adopting quality criteria...
- An alternative to the hand searching gold standard: validating methodological search filters using relative recallMargaret Sampson
Chalmers Research Group, Children s Hospital of Eastern Ontario Research Institute, Canada
BMC Med Res Methodol 6:33. 2006..We demonstrate the feasibility of using relative recall of included studies from multiple systematic reviews to validate methodological search filters as an alternative to validation against a gold standard formed through hand searching...
- Brazilian knowledge production in the field of child and adolescent healthDanilo Blank
Departamento de Pediatria, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
J Pediatr (Rio J) 82:97-102. 2006....
- Extraction of biological interaction networks from scientific literatureAndre Skusa
NRW International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Postfach 10 01 31, D 33501 Bielefeld, Germany
Brief Bioinform 6:263-76. 2005..This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature...
- PSE: a tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywordsTakashi Yoneya
Pharmaceutical Division, Kirin Brewery Co, Ltd, 3 Miyahara, Takasaki, Gunma 370 1295, Japan
BMC Bioinformatics 6:295. 2005..We usually have to repeatedly enter keywords in a trial-and-error manner to extract useful records. Software which can reduce such a laborious task is therefore required...
- Information retrieval and knowledge discovery utilising a biomedical Semantic WebSougata Mukherjea
IBM India Research Laboratory, Block I, Indian Institue of Technology, Hauz Khas, New Delhi 110016, India
Brief Bioinform 6:252-62. 2005..Finally, some of the challenges that have to be addressed to make the vision of a biomedical Semantic Web a reality are discussed...
- Hairpins in bookstacks: information retrieval from biomedical textHagit Shatkay
School of Computing, Queen s University, Kingston, Ontario, K7L 3N6, Canada
Brief Bioinform 6:222-38. 2005..This paper introduces the basics of information retrieval, discusses its applications in biomedicine, and presents traditional and non-traditional ways in which it can be used...
- A survey of the use of electronic scientific information resources among medical and dental studentsKalle Romanov
Research and Development Unit for Medical Education, University of Helsinki, P O Box 63, FIN 00014, Helsinki, Finland
BMC Med Educ 6:28. 2006..To evaluate medical and dental students' utilization of electronic information resources...
- Errors in search strategies were identified by type and frequencyMargaret Sampson
Chalmers Research Group, Children s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
J Clin Epidemiol 59:1057-63. 2006..Errors in the electronic search strategy of a systematic review may undermine the integrity of the evidence base used in the review. We studied the frequency and types of errors in reviews published by the Cochrane Collaboration...
- NATIONAL INFORMATION RESOURCE ON ETHICS & HUMAN GENETICSMargaret Little; Fiscal Year: 2010..To support the retrieval of these materials in the following bibliographic databases: Genetics and Ethics, ETHX on the Web, PubMed, and LOCATORplus;(all bibliographic records that refer to ..
- HAN Digital Library of Electronic Resources and ServicesTHEA CHESLEY; Fiscal Year: 2003..by adding to the Training & Resource Center Library resource sharing hub on the agency Intranet more bibliographic databases and full-text electronic library resources...
- END USER PROGRAM AT CENTRAL MAINE MEDICAL CENTERMARYANNE GREVEN; Fiscal Year: 1990..and tutorial labs, which would enable end-users to confidently perform successful searches of select bibliographic databases. The CD-ROM would offer end-users state-of-the-art technology in online searching, thereby making the ..
- NEW MODEL AND APPROACH TO RETRIEVAL SYSTEM EVALUATIONWilliam Hersh; Fiscal Year: 1999..While clinical information retrieval (IR) systems continue to proliferate, with the growing ubiquity of bibliographic databases and the explosion of hypermedia resources on the Internet and World Wide Web, most IR evaluation is still ..
- Enhancing Internet Access to Health-Related ResourcesMargaret Alexander; Fiscal Year: 2003The primary goals of this project are to: 1) enhance access to web-based health-related bibliographic databases, software, and Internet-assisted instructional programs; and 2) provide hardware needed to support access to these health-..
- Tool to Integrate Genomic and Proteomic Data of AgingZOE LACROIX; Fiscal Year: 2002..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
- Assisting Systematic Review Preparation Using Automated Document ClassificationAaron Cohen; Fiscal Year: 2009..Since up-to-date systematic reviews are essential for establishing widespread high quality practice standards and guidelines, the overall public health will benefit from this work. ..
- Caries Risk Assessment Instrument for Young AdultsGeorge Stookey; Fiscal Year: 2005..Future large-scale investigations will be undertaken to validate the merits of the instrument. ..
- Planning Grant for Xylitol Trial in Caries-Active AdultsJames Bader; Fiscal Year: 2005....
- Duplicate Article/Plagiarism DiscoveryHarold Garner; Fiscal Year: 2009..4) Create a secure resource that is available and open to all journals/reviewers, thus enabling them to estimate novelty and probable overlap with previous publications prior to acceptance. ..
- Activating Consumers to Exercise in Community Psychiatry Through Peer Support.Gail Daumit; Fiscal Year: 2008..This study will provide important data for future work to reduce cardiovascular risk and improve health in persons with SMI. [unreadable] [unreadable] [unreadable]..
- The Role of Inflammation and Parity on GDM and Type 2 DMWanda Nicholson; Fiscal Year: 2008..This award will give Dr. Nicholson the dedicated time and experience she needs to develop into an independent clinical investigator [unreadable] [unreadable]..
- Improving the Quality of News Reporting on MedicineLisa Schwartz; Fiscal Year: 2006..abstract_text> ..
- Toward Evidence Based Treatments to Reduce DUI RelapseHoward Shaffer; Fiscal Year: 2006..By identifying risk factors associated with relapse, this study will provide the foundation for new evidence-based treatment efforts that can curtail the rate of DUI [reoffense.] ..
- Development of QLF Handpiece for Early Caries DetectionGeorge Stookey; Fiscal Year: 2006..unreadable] [unreadable]..
- CLINICAL SEARCH RETRIEVAL FROM FOUR ELECTRONIC DATABASESR Haynes; Fiscal Year: 2007..of clinically relevant and scientifically sound reports from large, general purpose, biomedical research bibliographic databases such as MEDLINE...
- Achieving Healthy Lifestyles in Psych RehabilitationGail Daumit; Fiscal Year: 2007..This R34 will provide valuable pilot data for future work to improve healthy lifestyles and reduce chronic medical illness in people with SMI. ..
- THE SLEEP HEART HEALTH STUDYNaresh Punjabi; Fiscal Year: 2007..Accomplishing these goals will provide important information concerning the public health impact of SDB. ..
- The Role of Microsatellite Instability in CancerHarold Garner; Fiscal Year: 2005..We will also (Aim 3) investigate the effects of these mutations identified in Aim 2 on splicing by correlating them with the results of a quantitative global survey of splicing isoforms. ..
- The Status and Future of Acupuncture Research: 10 Years Post-NIH Consensus ConferLixing Lao; Fiscal Year: 2007..The proposed conference will do so. [unreadable] [unreadable] [unreadable] [unreadable]..
- ROLE OF DENTIN PHOSPHOPROTEIN IN DENTIN REMINERALIZATIONBRIAN CLARKSON; Fiscal Year: 2001..Ultimately, once the DPP's and their activity (for example, initiating or blocking mineral formation) have been identified they can be used in optimizing the repair of diseased and/or compromised dental hard tissues. ..
- SOFTWARE AND INSTRUMENTATION TO IDENTIFY CANCER GENESHarold Garner; Fiscal Year: 2002..This will integrate our system with current major technologies to produce a tool that should be widely available in translational and clinical trials cancer research. ..
- St. John's Wort for tobacco cessationAmit Sood; Fiscal Year: 2006..This study is anticipated to provide the data needed to develop a larger randomized controlled clinical trial submitted through the R01 funding mechanism to NCCAM. [unreadable] [unreadable]..
- EARLY IDENTIFICATION AND TREATMENT OF SLEEP APNEANaresh Punjabi; Fiscal Year: 2003..Punjabi the opportunity to reach his full potential as a clinical investigator. ..
- Conflict of Interest in Clinical Practice Guideline DevelopmentSusan L Norris; Fiscal Year: 2010..Understanding the impact of industry relationships will help guideline sponsors to develop appropriate policies for managing conflict of interest. ..
- Longtitudinal Changes in Sleep Structure: Implications for Health OutcomesNaresh Punjabi; Fiscal Year: 2010....
- HERMES - Help physicians to Extract and aRticulate Multimedia information from liHong Yu; Fiscal Year: 2009..5) Design a usability study to measure efficacy, accuracy and perceived ease of use of HERMES and to compare HERMES with other information systems. ..
- Endotoxin, Obesity, and Asthma in NYC Head StartJudith Jacobson; Fiscal Year: 2005..We will also conduct environmental sampling within the Head Start centers twice a year. Our goal is to identify risk factors that interventions can target to lighten the burden of asthma on school-age children. ..
- MENTAL HEALTH PREVENTION PROJECT: HELPING-U-GROW (HUGS)Harolyn Belcher; Fiscal Year: 2004..Videotaped assessments of the parent-child interaction will be conducted. Pre- and post intervention evaluations will include child and parent measures. ..
- CHILDREN WITH DRUG EXPOSURE: BEHAVIOR AND MRI STUDYHarolyn Belcher; Fiscal Year: 2004..abstract_text> ..
- Domestic Violence Enhanced Home Visitation Program-DOVEPHYLLIS WILLIAMS SHARPS; Fiscal Year: 2010..abstract_text> ..
- Gabapentin for Smoking AbstinenceAmit Sood; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- A Framework Based Clinical Documentation Evaluation MethodSAMUEL T ROSENBLOOM; Fiscal Year: 2010..The proposed project will transition the PI from his current National Library of Medicine supported period of career development to an independent informatics investigator. ..
- Operational Definition of Chronic Disability in the National Long-Term Care SurveElena Erosheva; Fiscal Year: 2008..Findings of this study will benefit secondary users of the NLTCS data and future designers of longitudinal surveys that aim to track chronic disability status of the elderly over time. [unreadable] [unreadable] [unreadable] [unreadable]..
- Columbia-GHI Consortium for Claims-Based Cancer StudiesSTEVEN STELLMAN; Fiscal Year: 2007..unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable] [unreadable]..
- Preventable Mortality in Maryland Medicaid SMIGail Daumit; Fiscal Year: 2009....
- Preparing Caregivers for the Death of their Loved OneRandy Hebert; Fiscal Year: 2007..This award will facilitate the candidate's transition to an independent researcher and will lead to future studies of interventions designed to improve the well-being of family caregivers. ..
- MENTAL & SOMATIC ILLNESS: NEEDS, SERVICES, AND OUTCOMESGail Daumit; Fiscal Year: 2004..Daumit the experience and tools she needs to develop into an independent clinician research in the epidemiology and health services research of mental disorders. ..
- PREVENTION OF EARLY CHILDHOOD CARIES IN MEDICAL PRACTICER Rozier; Fiscal Year: 2005..We will do a limited assessment of the cost pe oral health- related quality of life. ..
- The Effectiveness of Treatment for Adult PeriodontitisPhilippe Hujoel; Fiscal Year: 2006..This information can help determine in what area of periodontal research definitive clinical trials may offer the greatest contribution. ..
- NMR HIGH SENSITIVITY MOLECULAR STRUCTURE DETERMINATIONREINHARD DUNKEL; Fiscal Year: 2004..It further aims to automate molecular structure determinations. Molecular features insufficiently characterized by the input data can be reported for further human inspection. ..
- Effects of aging on sleep architectureNaresh Punjabi; Fiscal Year: 2006..unreadable] [unreadable]..
- Prediciting Severe Neonatal HyperbilirubinemiaRon Keren; Fiscal Year: 2007....
- Stress Reactivity & Protective Factors in SchizophreniaJoseph Ventura; Fiscal Year: 2003..abstract_text> ..
- Cohort Study of Nitrate Exposure, MHG, and HealthCatherine Zeman; Fiscal Year: 2004..of nitrate/nitrite containing waters and the overall health effects as they may reflect on the current maximum contaminant level, MCL of 10 ppm (mg/I) nitrate/nitrogen, a level that was set without consideration of a safety factor ..
- FAMILY, AUTONOMY AND SELF-CARE IN ADOLESCENTS WITH IDDMCarol Dashiff; Fiscal Year: 2003..Model fit will be evaluated by several methods, including goodness of fit and diagnostic plots of individual subject slopes. ..
- Efficacy of Acupuncture in Treating Urinary IncontinenceSandra Engberg; Fiscal Year: 2009..abstract_text> ..
- Chiropractic, Medication, and Self-care for Neck PainGert Bronfort; Fiscal Year: 2005..It will also provide clinically useful information for health care practitioners, policy makers and, most importantly, those who suffer from this painful and costly condition. ..
- Clinical Models Workshop:Remin-Demin, Precavity, CariesGeorge Stookey; Fiscal Year: 2005..The meeting will be held on July 3-5, 2005 in the Downtown Marriott Hotel in Indianapolis, Indiana, immediately prior to the annual ORCA (European Organization for Caries Research) meeting. ..
- Optically enhanced dental sealants to indicate placement and material conditionGeorge Stookey; Fiscal Year: 2006..unreadable] 3) An optically doped sealant combines the efficacy advantages of a clear sealant with the visibility advantages of an opaque sealant. [unreadable] [unreadable]..
- AFM and CFM Study of the Etiology of FluorosisBRIAN CLARKSON; Fiscal Year: 2007..This explanation may allow therapies or treatments to be devised that will prevent the deleterious effects of fluoride and let it be administered at levels, which will cause a greater reduction in caries. ..
- HOMEBOUND ELDERLY--MAINTAINING POSTTREATMENT CONTINENCESandra Engberg; Fiscal Year: 2002..10) Explore the development of a predictive model of patients who relapse during follow-up. ..
- Multifamily Group Autonomy Support Psychoeducation for Patents and Middle AdolescCAROL JEAN DASHIFF; Fiscal Year: 2010....
- Automated Literature Mining for Validation of High-Throughput Function PredictionKARIN MARIA VERSPOOR; Fiscal Year: 2010..It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction ..
- Clinical Ratings of Neurocognition (CRON)Joseph Ventura; Fiscal Year: 2007..The proposed developments are urgently needed to continue the momentum established by the MATRICS initiative, and facilitate regulatory acceptance and clinical awareness of new treatments for CIAS. [unreadable] [unreadable] [unreadable]..
- The Caring~web: Web-based Support for Stroke CaregiversLinda Pierce; Fiscal Year: 2004..Study outcomes have the potential to direct healthcare professionals in designing programs of care for persons with stroke and their caregivers. ..
- Motivational Feedback to Increase Walking AdherenceCaroline Richardson; Fiscal Year: 2008..Richardson will acquire the skills and knowledge to become an independent investigator and a leader in the field of physical activity promotion research for patients with cardiovascular disease. ..