Summary: A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
Publications231 found, 100 shown here
- Searching the MEDLINE literature database through PubMed: a short guideEdith Motschall
Institut für Medizinische Biometrie und Medizinische Informatik, Universitat Freiburg, Germany
Onkologie 28:517-22. 2005..One of the interfaces for searching Medline is PubMed, provided by the NLM for free access via the Internet (www.pubmed.gov)...
- The US National Library of Medicine in the 21st century: expanding collections, nontraditional formats, new audiencesEve Marie Lacroix
National Library of Medicine, Bethesda, MD 20894, USA
Health Info Libr J 19:126-32. 2002..A national library such as the NLM has as much an archival responsibility for this electronic information as for centuries-old printed and manuscript historical treasures...
- Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknessesMatthew E Falagas
Alfa Institute of Biomedical Sciences AIBS, 9 Neapoleos St, 151 23 Marousi, Greece
FASEB J 22:338-42. 2008..We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar...
- Efficient bibliographic searches on allergology using PubMedJ M Sáez Gómez
Department of Social and Health Sciences University of Murcia Medical School Spain
Allergol Immunopathol (Madr) 35:264-75. 2007b>PubMed is the most important of the non-specialized databases on biomedical literature...
- New year, new PubMedE Giglia
University of Turin, Turin, Italy
Eur J Phys Rehabil Med 45:155-9. 2009Aim of this contribution was to present the latest additions to the worldwide known PubMed interface, concerning a better visualization of results list; a new format for the Advanced search which has merged the old labels' options; new ..
- The quality of reports of randomised trials in 2000 and 2006: comparative study of articles indexed in PubMedSally Hopewell
Centre for Statistics in Medicine, University of Oxford, Linton Road, Oxford OX2 6UD
BMJ 340:c723. 2010To examine the reporting characteristics and methodological details of randomised trials indexed in PubMed in 2000 and 2006 and assess whether the quality of reporting has improved after publication of the Consolidated Standards of ..
- SciMiner: web-based literature mining tool for target identification and functional enrichment analysisJunguk Hur
Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
Bioinformatics 25:838-40. 2009..SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input...
- A major pitfall in the search strategy on PubMedGhazi O Tadmouri
Department of Biology, Bioinformatics Unit, Fatih University, Buyukcekmece, Istanbul, Turkey
Saudi Med J 25:7-10. 2004
- Comparison of PubMed and Google Scholar literature searchesMichael E Anders
Department of Respiratory and Surgical Technologies, College of Health Related Professions, University of Arkansas for Medical Sciences, 737, 4301 West Markham Street, Little Rock, AR 72205, USA
Respir Care 55:578-83. 2010....
- Complex event extraction at PubMed scaleJari Björne
Department of Information Technology, University of Turku, Turku, Finland
Bioinformatics 26:i382-90. 2010..A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction...
- Development of a methodological PubMed search filter for finding studies on measurement properties of measurement instrumentsCaroline B Terwee
Department of Epidemiology and Biostatistics and the EMGO Institute for Health and Care Research, VU University Medical Center, Van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
Qual Life Res 18:1115-23. 2009..a highly sensitive search filter for finding studies on measurement properties of measurement instruments in PubMed and a more precise search filter that needs less abstracts to be screened, but at a higher risk of missing ..
- Recommending MeSH terms for annotating biomedical articlesMinlie Huang
State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua University, Beijing, PR China
J Am Med Inform Assoc 18:660-7. 2011..Here, we report a novel approach to facilitate MeSH indexing, a challenging task of assigning MeSH terms to MEDLINE citations for their archiving and retrieval...
- A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactionsJörg Hakenberg
Computer Science Department, Arizona State University, 699 S Mill Ave, Tempe, AZ 85281, USA
J Biomed Inform 45:842-50. 2012..Here, we seek to aid researchers, database curators, and clinicians in their search for relevant information by automatically extracting these data from literature...
- Medical literature searches: a comparison of PubMed and Google ScholarEva Nourbakhsh
Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
Health Info Libr J 29:214-22. 2012..Medical literature searches provide critical information for clinicians. However, the best strategy for identifying relevant high-quality literature is unknown...
- Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMedCarlijn R Hooijmans
Radboud University Nijmegen Medical Centre, Central Animal Laboratory and 3R Research Centre, Geert Grooteplein Noord 29, route 231, Nijmegen, The Netherlands
Lab Anim 44:170-5. 2010..In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies...
- PubMed and beyond: a survey of web tools for searching biomedical literatureZhiyong Lu
National Center for Biotechnology Information NCBI, National Library of Medicine, Bethesda, MD 20894, USA
Database (Oxford) 2011:baq036. 2011..In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement...
- Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2DYun Niu
Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G1L7, Canada
Bioinformatics 26:111-9. 2010..More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction...
- Linking ClinicalTrials.gov and PubMed to track results of interventional human clinical trialsVojtech Huser
Laboratory for Informatics Development, NIH Clinical Center, Bethesda, Maryland, United States of America
PLoS ONE 8:e68409. 2013..In an effort to understand how results of human clinical trials are made public, we analyze a large set of clinical trials registered at ClinicalTrials.gov, the world's largest clinical trial registry...
- GeneView: a comprehensive semantic search engine for PubMedPhilippe Thomas
Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
Nucleic Acids Res 40:W585-91. 2012..GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts...
- Egyptian biomedical publications in PubMed, 1996-2005Mustafa Afifi
Department of Non communicable Diseases Control, Ministry of Health HQ, Muscat, Oman
J Egypt Public Health Assoc 82:91-104. 2007This study aims to analyze ten-year (1996-2005) biomedical publications produced in Egypt in PubMed. A Medline search was performed on 12th December 2006 with the aid of PubMed to have the total number of publications of authors ..
- Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer predictionDi Zhao
Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
J Biomed Inform 44:859-68. 2011In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction...
- Event extraction for systems biology by text mining the literatureSophia Ananiadou
University of Manchester, Manchester M13 9PL, UK
Trends Biotechnol 28:381-90. 2010..The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states...
- SemMedDB: a PubMed-scale repository of biomedical semantic predicationsHalil Kilicoglu
Lister Hill National Center for Biomedical Communications, National Library of Medicine, Bethesda, MD 20894, USA
Bioinformatics 28:3158-60. 2012..a repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations...
- Annotating genes and genomes with DNA sequences extracted from biomedical articlesMaximilian Haeussler
Faculty of Life Sciences, University of Manchester, Manchester, UK
Bioinformatics 27:980-6. 2011..Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study...
- Discovering and visualizing indirect associations between biomedical conceptsYoshimasa Tsuruoka
School of Information Science, Japan Advanced Institute of Science and Technology JAIST, Nomi, Japan
Bioinformatics 27:i111-9. 2011..Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner...
- PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolitesDean Cheng
Department of Computing Science, University of Alberta, Canada
Nucleic Acids Res 36:W399-405. 2008..Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearch...
- UKPMC: a full text article resource for the life sciencesJohanna R McEntyre
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 39:D58-65. 2011UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository...
- Identifying diagnostic studies in MEDLINE: reducing the number needed to readLucas M Bachmann
University of Zurich, Zurich, Switzerland
J Am Med Inform Assoc 9:653-8. 2002The search filters in PubMed have become a cornerstone in information retrieval in evidence-based practice. However, the filter for diagnostic studies is not fully satisfactory, because sensitive searches have low precision...
- Finding complex biological relationships in recent PubMed articles using Bio-LDAHuijun Wang
School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
PLoS ONE 6:e17243. 2011..This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing...
- Utilization of the PICO framework to improve searching PubMed for clinical questionsConnie Schardt
Medical Center Library, Duke University, Durham, North Carolina 27710, USA
BMC Med Inform Decis Mak 7:16. 2007..Many questions go unanswered, however, due to lack of skills in formulating questions, crafting effective search strategies, and accessing databases to identify best levels of evidence...
- PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queriesAdriano Barbosa-Silva
Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rössle Strasse, 10, D 13125, Berlin, Germany
BMC Bioinformatics 12:435. 2011..Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-..
- LitInspector: literature and signal transduction pathway mining in PubMed abstractsMatthias Frisch
Genomatix Software, 80335 Munich, Germany
Nucleic Acids Res 37:W135-40. 2009LitInspector is a literature search tool providing gene and signal transduction pathway mining within NCBI's PubMed database...
- Overview of BioCreative II gene normalizationAlexander A Morgan
Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA
Genome Biol 9:S3. 2008..For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes...
- Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstractsChih Hsuan Wei
National Center for Biotechnology Information NCBI, National Library of Medicine NLM, 8600 Rockville Pike, Bethesda, MD 20894, USA
Database (Oxford) 2012:bas041. 2012..participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation...
- Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic informationSun Kim
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Database (Oxford) 2012:bas042. 2012..Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team...
- Find duplicates among the PubMed, EMBASE, and Cochrane Library Databases in systematic reviewXingshun Qi
Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi an, China Department of Gastroenterology, No 463 Hospital of Chinese PLA, Shenyang, China
PLoS ONE 8:e71838. 2013..This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates...
- Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfactionAurélie Névéol
National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Biomed Inform 44:310-8. 2011..Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories...
- Biomedical knowledge navigation by literature clusteringYasunori Yamamoto
Department of Computational Biology, University of Tokyo, Kibanto CB01, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8561, Japan
J Biomed Inform 40:114-30. 2007..We developed such a system called McSyBi. It accepts a set of citation data retrieved with PubMed and hierarchically and non-hierarchically clusters them based on the titles and the abstracts using statistical ..
- Google Scholar versus PubMed in locating primary literature to answer drug-related questionsMaisha Kelly Freeman
McWhorter School of Pharmacy, Samford University, Birmingham, AL 35229, USA
Ann Pharmacother 43:478-84. 2009Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown.
- PPI finder: a mining tool for human protein-protein interactionsMin He
Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
PLoS ONE 4:e4554. 2009..One of the most common applications is to mine protein-protein interactions (PPIs) from PubMed abstracts...
- PubTator: a web-based text mining tool for assisting biocurationChih Hsuan Wei
National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 41:W518-22. 2013..PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text ..
- 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
- Impact of PubMed search filters on the retrieval of evidence by physiciansSalimah Z Shariff
Division of Nephrology, University of Western Ontario, London, Ont
CMAJ 184:E184-90. 2012Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles...
- BioNØT: a searchable database of biomedical negated sentencesShashank Agarwal
Medical Informatics, College of Engineering and Applied Sciences, University of Wisconsin Milwaukee, 3200 N, Cramer St, Milwaukee, WI 53201 0784, USA
BMC Bioinformatics 12:420. 2011..We report on the development of BioNØT, a database of negated sentences that can be used to extract such negated events...
- Extraction of data deposition statements from the literature: a method for automatically tracking research resultsAurélie Névéol
National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
Bioinformatics 27:3306-12. 2011..For this reason, it is important to be able to identify instances of data production and deposition for potential re-use. Herein, we report on the automatic identification of data deposition statements in research articles...
- Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstractsLijing Xu
Bioinformatics Program, University of Memphis, Memphis, Tennessee, United States of America
PLoS ONE 6:e18851. 2011..GCAT can complement other gene set enrichment approaches by determining the overall functional cohesion of data sets, taking into account both explicit and implicit gene interactions reported in the biomedical literature...
- Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMedNicolas Griffon
CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage, 1 rue de Germont, 76031 Rouen Cedex, France
BMC Med Inform Decis Mak 12:12. 2012b>PubMed is the main access to medical literature on the Internet...
- Improving accuracy for identifying related PubMed queries by an integrated approachZhiyong Lu
National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Biomed Inform 42:831-8. 2009b>PubMed is the most widely used tool for searching biomedical literature online...
- Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene setsSujoy Roy
Bioinformatics Program, University of Memphis, Memphis, TN 38152, USA
BMC Bioinformatics 12:S19. 2011....
- Analysis of queries sent to PubMed at the point of care: observation of search behaviour in a medical teaching hospitalArjen Hoogendam
Department of Medicine, Division of General Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
BMC Med Inform Decis Mak 8:42. 2008The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted...
- Searching for medical information online: a survey of Canadian nephrologistsSalimah Z Shariff
Department of Epidemiology and Biostatistics, University of Western Ontario, London, Ontario, Canada
J Nephrol 24:723-32. 2011..Physicians often search for information to improve patient care. We evaluated how nephrologists use online information sources for this purpose...
- Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filtersCynthia Lokker
Health Information Research Unit, McMaster University, Faculty of Health Sciences, Hamilton, Ontario, Canada
J Am Med Inform Assoc 18:652-9. 2011..objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters.
- PIE the search: searching PubMed literature for protein interaction informationSun Kim
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioinformatics 28:597-8. 2012..However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results ..
- PubDNA Finder: a web database linking full-text articles to sequences of nucleic acidsMiguel Garcia-Remesal
Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Campus de Montegacedo S N, Boadilla del Monte, Madrid, Spain
Bioinformatics 26:2801-2. 2010PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them...
- Geography of Africa biomedical publications: an analysis of 1996-2005 PubMed papersOlalekan A Uthman
Center for Evidence Based Global Health, Save the Youth Initiative, Nigeria
Int J Health Geogr 6:46. 2007..We sought to examine trends and contribution of different Africa subregions and individual countries as represented by the articles indexed by PubMed between 1996 and 2005.
- Compounds In Literature (CIL): screening for compounds and relatives in PubMedBjörn A Grüning
Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert Ludwigs University, Freiburg, Germany
Bioinformatics 27:1341-2. 2011..and similar structures in over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL's pre-calculated database contains more than 56 million parent compound-abstract relations...
- Dragon TF Association Miner: a system for exploring transcription factor associations through text-miningHong Pan
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
Nucleic Acids Res 32:W230-4. 2004We present Dragon TF Association Miner (DTFAM), a system for text-mining of PubMed documents for potential functional association of transcription factors (TFs) with terms from Gene Ontology (GO) and with diseases...
- On the persistence of supplementary resources in biomedical publicationsNicholas R Anderson
Division of Biomedical Health Informatics, University of Washington, USA
BMC Bioinformatics 7:260. 2006..One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers...
- MiSearch adaptive pubMed search toolDavid J States
Department of Human Genetics, National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
Bioinformatics 25:974-6. 2009..acquired during browsing and used to dynamically update a likelihood model that includes authorship, journal and PubMed indexing information...
- Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMSHwanjo Yu
CSE Department, POSTECH, Pohang, South Korea
BMC Bioinformatics 11:S6. 2010Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results...
- The publication echo: effects of retrieving literature in PubMed by year of publicationCord Spreckelsen
Institut for Medical Informatics, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
Int J Med Inform 79:297-303. 2010In PubMed search forms, the publication date refers to both the date of electronic and printed publication. This fact is documented in PubMed, but difficult to anticipate by the users and can provoke misinterpretations of search results...
- A PubMed-wide associational study of infectious diseasesVitali Sintchenko
Centre for Health Informatics, University of New South Wales, Sydney, New South Wales, Australia
PLoS ONE 5:e9535. 2010..A significant proportion of the more than 18 million manuscripts indexed in the PubMed database describe infectious disease syndromes and various infectious agents...
- Searching the medical literature using PubMed: a tutorialJon O Ebbert
Division of Community Internal Medicine, Mayo Clinic, MN 55905, USA
Mayo Clin Proc 78:87-91. 2003..b>PubMed (http://www.pubmedgov) provides free access to the largest biomedical resource available and is updated daily...
- Searching the literature using medical subject headings versus text word with PubMedAngela A Chang
Department of Otolaryngology Head and Neck Surgery, University of California, San Diego, and the VA San Diego Healthcare System, San Diego, California, USA
Laryngoscope 116:336-40. 2006..study was conducted to investigate the performance of two search strategies in the retrieval of information from the National Library of Medicine (NLM) on otolaryngology-head and neck surgery related conditions and diagnoses using PubMed.
- GoGene: gene annotation in the fast laneConrad Plake
Biotechnology Center, Technische Universitat Dresden, 01307 Dresden, Germany
Nucleic Acids Res 37:W300-4. 2009..associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries...
- Speed, accuracy, and confidence in Google, Ovid, PubMed, and UpToDate: results of a randomised trialRobert H Thiele
Department of Anesthesiology, University of Virginia Health System, PO Box 800710, Charlottesville, VA 22908, USA
Postgrad Med J 86:459-65. 2010..It is thus increasingly critical for physicians to acquire a working knowledge of biomedical informatics...
- Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstractsJiao Li
State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua University, Beijing, China
PLoS Comput Biol 5:e1000450. 2009..Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular ..
- PuReD-MCL: a graph-based PubMed document clustering methodologyT Theodosiou
Department of Informatics, Aristotle University of Thessalonica, P O Box 54124, Thessalonica, Greece
Bioinformatics 24:1935-41. 2008Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organizing and analyzing such textual knowledge...
- A bibliometric study of scientific literature on obesity research in PubMed (1988-2007)J Vioque
Departamento de Salud Publica, Universidad Miguel Hernandez, San Juan de Alicante, Spain
Obes Rev 11:603-11. 2010This article describes a bibliometric review of the publications on obesity research in PubMed over the last 20 years. We used Medline via the PubMed online service of the US National Library of Medicine from 1988 to 2007...
- pubmed2ensembl: a resource for mining the biological literature on genesJoachim Baran
Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
PLoS ONE 6:e24716. 2011..For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions...
- PubMeth: a cancer methylation database combining text-mining and expert annotationMaté Ongenaert
Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B 9000 Ghent, Belgium
Nucleic Acids Res 36:D842-6. 2008..The database is freely accessible at http://www.pubmeth.org. PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts...
- Conducting literature searches on Ayurveda in PubMed, Indian, and other databasesSaravu R Narahari
Institute of Applied Dermatology, Kasaragod, Kerala, India
J Altern Complement Med 16:1225-37. 2010..searches for articles on Ayurveda provide special challenges, since many of the Indian journals in which such articles appear are not indexed by current medical databases such as PubMed and Cochrane Central Register of Controlled Trials.
- PubCrawler: keeping up comfortably with PubMed and GenBankKarsten Hokamp
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
Nucleic Acids Res 32:W16-9. 2004..It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries...
- SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary studyMichael Muin
Office of High Performance Computing and Communications, National Library of Medicine, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
- Mapping the history and current situation of research on John Cunningham virus - a bibliometric analysisHua Chuan Zheng
Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, Shenyang, PR China
BMC Infect Dis 9:28. 2009..However, no bibliometric investigation has been reported to guide the researchers and potential readers...
- Answers to questions posed during daily patient care are more likely to be answered by UpToDate than PubMedArjen Hoogendam
Department of Medicine, Division of General Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
J Med Internet Res 10:e29. 2008UpToDate and PubMed are popular sources for medical information. Data regarding the efficiency of PubMed and UpToDate in daily medical care are lacking.
- EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstractsSüveyda Yeniterzi
Sabanci University, Istanbul, Turkey
BMC Bioinformatics 10:S2. 2009..In this paper, therefore, we describe an unique method, termed as EnzyMiner, which automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability and/or the activity ..
- Using advanced search tools on PubMed for citation retrievalAmit Sood
Division of General Internal Medicine, Mayo Clinic College of Medicine, Rochester, Minn 55905, USA
Mayo Clin Proc 79:1295-9; quiz 1300. 2004b>PubMed (www.pubmed.gov) provides health care professionals with free access to one of the largest searchable biomedical databases available...
- Evaluating relevance ranking strategies for MEDLINE retrievalZhiyong Lu
NCBI NLM NIH, 8600 Rockville Pike, Bethesda, MD 20852, USA
J Am Med Inform Assoc 16:32-6. 2009..Furthermore, the authors use the reverse chronological order-PubMed's default display option-as a baseline for comparison...
- Search strategies for population and social subjects in a medical school curriculumJonathan D Eldredge
University of New Mexico, MSC09 5100, Albuquerque, NM, 87131 0001 USA
Med Ref Serv Q 23:35-47. 2004..describes strategies developed for medical students to conduct Specific (as opposed to Sensitive) searches in PubMed so they can quickly locate several relevant references to articles on the population and social aspects of ..
- Optimization of the PubMed Automatic Term MappingBenoit Thirion
CISMeF, Rouen University Hospital and GCSIS, TIBS, LITIS EA 4108, Biomedical Research Institute, 76031 Rouen, France
Stud Health Technol Inform 150:238-42. 2009b>PubMed, freely available on the internet, is the best known database for medical information. We propose a method of optimization of the PubMed Automatic Term Mapping (ATM) that includes MeSH terms...
- Searching the medical literatureDonald A B Lindberg
N Engl J Med 354:2393; author reply 2393. 2006
- Enriching PubMed related article search with sentence level co-citationsNam Tran
Department of Pathology, Yale University, New Haven, CT 06520, USA
AMIA Annu Symp Proc 2009:650-4. 2009b>PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature...
- A bibliometric analysis of tuberculosis research indexed in PubMed, 1997-2006J M Ramos
Infectious Diseases Unit, Internal Medicine Service, Hospital General Universitario de Elche, Alicante, Spain
Int J Tuberc Lung Dis 12:1461-8. 2008To describe a bibliometric review of the literature on tuberculosis (TB) research indexed in PubMed over a 10-year period.
- To compare PubMed Clinical Queries and UpToDate in teaching information mastery to clinical residents: a crossover randomized controlled trialLadan Sayyah Ensan
Center for Educational Research in Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
PLoS ONE 6:e23487. 2011To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction.
- 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...
- Finding translational science publications in MEDLINE/PubMed with translational science filtersPaul Fontelo
National Library of Medicine, Bethesda, Maryland, USA
Clin Transl Sci 4:455-9. 2011Translational Science Search (TSS; http://tscience.nlm.nih.gov) is a web application for finding MEDLINE/PubMed journal articles that are regarded by their authors as novel, promising, or may have potential clinical application...
- Searching additional databases except PubMed are necessary for a systematic reviewMing Hua Zheng
Stroke 39:e139; author reply e140. 2008
- Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogensSam Zaremba
ERIC BRC, SRA International Inc, Global Health Sector, Rockville, MD 20852, USA
BMC Bioinformatics 10:177. 2009..Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process...
- Analysis of Saudi Medical Journal publications in PubMed, January 2001-November 2006Mustafa Afifi
Department of Non communicable Diseases Control, Ministry of Health HQ, PO Box 393, PC 113, Muscat, Oman
Saudi Med J 28:1145-7. 2007
- Analysis of citations to biomedical articles affected by scientific misconductAnne Victoria Neale
Department of Family Medicine and Public Health Sciences, Wayne State University School of Medicine, 101 E Alexandrine, 249, Detroit, MI 48201, USA
Sci Eng Ethics 16:251-61. 2010..Most articles affected by misconduct were published in basic science journals, and we found little cause for concern that such articles may have affected clinical equipoise or clinical care...
- GLAD4U: deriving and prioritizing gene lists from PubMed literatureJerome Jourquin
Department of Biomedical Informatics, Vanderbilt University School of Medicine, 400 Eskind Biomedical Library, 2209 Garland Avenue, Nashville, TN 37232, USA
BMC Genomics 13:S20. 2012..such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists...
- Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interfaceMichael Simon
School of Nursing, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, Kansas 66160, USA
BMC Med Res Methodol 10:76. 2010The identification of health services research in databases such as PubMed/Medline is a cumbersome task...
- PubMed on Tap: discovering design principles for online information delivery to handheld computersSusan E Hauser
Communications Engineering Branch, Lister Hill National Center for Biomedical Communications, NLM, NIH, Bethesda, MD 20894, USA
Stud Health Technol Inform 107:1430-3. 2004..Continued research is expected to discover additional user interface design principles as well as guidelines for results organization and system performance..
- Mental health publications from the Arab world cited in PubMed, 1987-2002M M Afifi
Department of Research and Studies, Ministry of Health, Muscat, Oman
East Mediterr Health J 11:319-28. 2005The study aimed to identify mental health publications in Arab countries cited in PubMed from 1987 to 2002 and to analyse the year of publication, journal and field of research, specifically for child and adolescent mental health studies...
- An examination of PubMed's ability to disambiguate subject queries and journal title queriesAida Marissa Smith
Loma Linda University, Del E Webb Memorial Library, 11072 Anderson Street, Loma Linda, California 92350, USA
J Med Libr Assoc 92:97-100. 2004
- Mapping of medical acronyms and initialisms to Medical Subject Headings (MeSH) across selected systemsMary Shultz
Library of the Health Sciences Urbana, University of Illinois at Chicago, 102 Medical Sciences Building, 506 South Mathews, Urbana, Illinois 61801, USA
J Med Libr Assoc 94:410-4. 2006..The purpose of this study is to evaluate how various MEDLINE Medical Subject Headings (MeSH) interfaces map acronyms and initialisms to the MeSH vocabulary...
- Systematic identification of pharmacogenomics information from clinical trialsJiao Li
National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Biomed Inform 45:870-8. 2012..This work has practical implications in enriching our existing knowledge on PGx gene-drug-disease relationships as well as suggesting crosslinks between ClinicalTrials.gov and other PGx knowledge bases...
- Literature search using PubMed: an essential tool for practicing evidence- based medicineA Sood
Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
J Assoc Physicians India 54:303-8. 2006Efficient literature search is essential to the practice of Evidence-Based Medicine. PubMed provides free access to one of the largest searchable biomedical databases...
- Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMedS G P Vellay
Accelrys Ltd, 334 Cambridge Science Park, Cambridge CB4 0WN, UK
Infect Disord Drug Targets 9:366-74. 2009..Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results...
- Documentation in pharmacovigilance: using an ontology to extend and normalize Pubmed queriesDenis Delamarre
INSERM U936, Universite Rennes 1, IFR 140, Rennes, France
Stud Health Technol Inform 160:518-22. 2010To assess and understand adverse drug reactions (ADRs), a systematic review of reference databases like Pubmed is a necessary and mandatory step in Pharmacovigilance...
- Improving CBF through direct control of CSF pulsationsMARK GREGORY LUCIANO; Fiscal Year: 2010....
- A Public Cannabinoid Molecular Information RepositoryXiang Qun Xie; Fiscal Year: 2007..Ultimately, this proposed research project will make a significant contribution by developing a tool and a medium for information exchange and data sharing among the scientific community and beyond. [unreadable] [unreadable]..
- Research Culture of Practice-Based Research NetworksANNE NEALE; Fiscal Year: 2007..A team of investigators from the PBRN Resource Center at Indiana University, and the Wayne State University Division of Practice-based Research will collaborate to ensure the success of the project. [unreadable] [unreadable] [unreadable]..
- Bell's Palsy-Randomized Clinical TrialJohn Neely; Fiscal Year: 2007..This revised planning grant application is to support necessary preparation for the multicenter trial. [unreadable] [unreadable] [unreadable]..
- A Toxicological Knowledge Base PrototypeNikolai Daraselia; Fiscal Year: 2007..and automatically updated) with information extracted from publicly available literature resources (such as Pubmed, ToxLine, and full-text journals) using extended MedScan technology. The value of the proposed system is two-fold...
- Correcting the Literature After Scienctific MisconductANNE NEALE; Fiscal Year: 2003..abstract_text> ..
- 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. ..
- Tools & Data Resources in Support of Structural GenomicsPHILIP BOURNE; Fiscal Year: 2006..The proposed public resource will complement the private software and data resulting from the individual structural genomics centers as they undertake competitive high throughput structure determination. ..
- Cultural Competency Training in Latino HealthDesiree Lie; Fiscal Year: 2008..A central web resource will disseminate case-based instruction and relevant pertinent research on health disparities. ..
- Integrated Neuroinformatics Resource for Alcoholism (IN*Lawrence Hunter; Fiscal Year: 2005..We believe the INRA will greatly enhance the Dace of discovery in the area of ethanol consumption and neuroadaptation to alcohol within the INIAC as well as the general research community. ..
- Mining slime mold for susceptibility genes to fungiArturo Casadevall; Fiscal Year: 2005..discoideum system will lead to the identification of genetic pathways that are not immediately obvious from standard fungal-macrophage experiments. ..
- PREVENTING CHRONIC WHIPLASH PAIN: BIOBEHAVIORAL APPROACHDENNIS TURK; Fiscal Year: 2005..The data from this trial will provide important information about the potential of early interventions to prevent chronic problems that afflict millions of MVA victims. ..
- Transcriptional Regulation of Mesoderm DevelopmentANN CORSI; Fiscal Year: 2005..New genes in the pathway that are identified in C elegans are predicted to be good candidates for the unknown genetic basis underlying these human disorders. ..
- High Dose Nicotine Patch Therapy for Spit Tobacco UsersJon Ebbert; Fiscal Year: 2004..Our goal is to reduce the prevalence of ST use and decrease the incidence of oropharyngeal cancer through the development of effective treatment options for ST users. ..
- 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. ..
- Protein Functional Site Characterization and AnalysisPhilip E Bourne; Fiscal Year: 2010..The results of this effort will be disseminated through the Protein Data Bank which is used by over 10,000 scientists every day. ..
- 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. ..
- Evaluating Nicotine Lozenges for Treatment of Smokeless Tobacco AddictionJon Ebbert; Fiscal Year: 2009..No drug therapies have been shown to be effective for helping smokeless tobacco users quit for good. The purpose of this study is to test drugs that can be used to help smokeless tobacco users quit for good. ..
- Single-Molecule Fluorophores for Cellular ImagingWILLIAM MOERNER; Fiscal Year: 2008..abstract_text> ..
- HERMES - Help physicians to Extract and aRticulate Multimedia information from liHong Yu; Fiscal Year: 2009..Although PubMed is frequently used by physicians in large hospitals, it does not return answers to specific questions...
- Transcriptional Regulation of Mesoderm DevelopmentANN CORSI; Fiscal Year: 2007..We expect because roundworm and human proteins are related, the information we learn will be relevant to humans and human disease. [unreadable] [unreadable] [unreadable]..
- 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. ..
- Single-Molecule Studies of Chaperonin MechanismWILLIAM MOERNER; Fiscal Year: 2006..The exploratory nature of this application arises from the fact that many of the assays proposed have not been previously utilized to explore chaperonin mechanisms. [unreadable] [unreadable] [unreadable]..
- Flexible NLP system for MEDLINE information extractionNikolai Daraselia; Fiscal Year: 2003..We will also extend our approach to other areas including pharmacogenomics and extraction of clinically relevant information. ..
- MOLECULAR CHARACTERIZATION OF C NEOFORMANS ANTIBODIESArturo Casadevall; Fiscal Year: 2006..These studies are expected to yield new insights on fundamental aspects of antibody function as well as practical information for the development of second generation antibody reagents for human therapy. ..
- ISMB 2005 Conf. Support for Students & Young ScientistsPHILIP BOURNE; Fiscal Year: 2005..This proposal seeks to assist them at this critical but resource-limited stage in their careers. ..
- NMR/COMPUTER MODELING FOR CANNABINOID LIGAND DESIGNXiang Qun Xie; Fiscal Year: 2002..Overall, the studies will provide insights into the design of a new generation of ligands possessing enhanced biological activity. ..
- Brief Dental Office Intervention with Tobacco QuitlineJon Ebbert; Fiscal Year: 2005..S. adult population smoking; and 3) 75% of smokers quitting for at least one day or longer because they are trying to quit. ..
- Development of Single-Biomolecule Optical ImagingWILLIAM MOERNER; Fiscal Year: 2004..abstract_text> ..
- Cerebral Blood Flow Response to Chronic HydrocephalusMark Luciano; Fiscal Year: 2004..Finally, the insights gained from these studies may have a broader application to other neuropathologies involving gradual compression or hypoxia. ..
- ANTICANCER DRUG EXPULSION IN SHED VESICLESGUS ROSANIA; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- PubAssist - an NLP-based document search systemNikolai Daraselia; Fiscal Year: 2005..Customers who install the server-based semantic indexing engine in addition to the PubAssist client will be able to process their proprietary documents and customize the NLP algorithm. ..
- S-Adenosyl Methionine(SAMe)Augmentation of SSRIs in MDDGeorge Papakostas; Fiscal Year: 2008..It is hoped that this project award will provide the critical fund of basic knowledge and practical experience necessary to aid the candidate in becoming an independent investigator in this area. ..
- Mediated Integration of Neuroscience ResourcesLuis Marenco; Fiscal Year: 2008..abstract_text> ..
- Advanced Isotope Aided NMR For CB2 Structural StudyXiang Qun Xie; Fiscal Year: 2005..The work accomplished through this proposed research can potentially make a significant contribution to cannabinoid research and NMR structural biology, as well as GPCRs in general. ..
- CLINICAL SEARCH RETRIEVAL FROM FOUR ELECTRONIC DATABASESR Haynes; Fiscal Year: 2007..g., sensitivity); and evaluating the usefulness of the clinical hedges in the intended users group, clinicians. [unreadable] [unreadable]..
- Development of an Electrokinetic Trap for Single Biomolecules in SolutionWILLIAM MOERNER; Fiscal Year: 2008..It is for this reason that this research represents a new and powerful potential advance for biomedical applications. [unreadable] [unreadable] [unreadable]..
- SUBGROUPS OF FMS--SYMPTOMS, BELIEFS & TAILORED TREATMENTDENNIS TURK; Fiscal Year: 2009..COMB treatment potentially produces the best overall outcome, since it incorporates both CR+ST, which is relevant to all participants, and ET, which is relevant to high fear participants. ..
- RESCUE: Randomized Evaluation of Patients with Stable Angina Comparing UtilizatioArthur E Stillman; Fiscal Year: 2010..Findings are expected to result in validation of an evolving new standard of care for patients with stable angina that takes advantage of CCTA to more cost effectively drive appropriate care. ..
- Database of Functional SNPs in Cancer-Related Environmentally Responsive GenesYong Zhu; Fiscal Year: 2009..Findings from this study will enhance the use of SNPs in future phenotypic studies and molecular epidemiologic approaches to address questions related to gene-environment interaction in disease risk estimate. ..