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.

Top Publications

  1. Yeniterzi S, Sezerman U. EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. BMC Bioinformatics. 2009;10 Suppl 8:S2 pubmed publisher
    ..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 ..
  2. Terwee C, Jansma E, Riphagen I, de Vet H. Development of a methodological PubMed search filter for finding studies on measurement properties of measurement instruments. Qual Life Res. 2009;18:1115-23 pubmed publisher
    ..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 ..
  3. Falagas M, Pitsouni E, Malietzis G, Pappas G. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J. 2008;22:338-42 pubmed
    ..We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar...
  4. Wang P, Morgan A, Zhang Q, Sette A, Peters B. Automating document classification for the Immune Epitope Database. BMC Bioinformatics. 2007;8:269 pubmed
    ..Improvements on the basic classifier performance were made by a) utilizing information stored in PubMed beyond the abstract itself b) applying standard feature selection criteria and c) extracting domain specific ..
  5. Qi X, Yang M, Ren W, Jia J, Wang J, Han G, et al. Find duplicates among the PubMed, EMBASE, and Cochrane Library Databases in systematic review. PLoS ONE. 2013;8:e71838 pubmed publisher
    ..Literatures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers...
  6. Griffon N, Chebil W, Rollin L, Kerdelhué G, Thirion B, Gehanno J, et al. Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMed. BMC Med Inform Decis Mak. 2012;12:12 pubmed publisher
    b>PubMed is the main access to medical literature on the Internet...
  7. Zhao D, Weng C. Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction. J Biomed Inform. 2011;44:859-68 pubmed publisher
    In 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...
  8. Kim S, Kwon D, Shin S, Wilbur W. PIE the search: searching PubMed literature for protein interaction information. Bioinformatics. 2012;28:597-8 pubmed publisher
    ..However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results ..
  9. Fang F, Steen R, Casadevall A. Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A. 2012;109:17028-33 pubmed publisher
    A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67...

More Information


  1. Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch T. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012;28:3158-60 pubmed publisher
    ..a repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations...
  2. Huser V, Cimino J. Linking and PubMed to track results of interventional human clinical trials. PLoS ONE. 2013;8:e68409 pubmed publisher
  3. Huser V, Cimino J. Precision and negative predictive value of links between and PubMed. AMIA Annu Symp Proc. 2012;2012:400-8 pubmed ( and PubMed. CT...
  4. Xu L, Furlotte N, Lin Y, Heinrich K, Berry M, George E, et al. Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstracts. PLoS ONE. 2011;6:e18851 pubmed publisher
    ..GCAT is freely available at ..
  5. Fleuren W, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, et al. CoPub update: CoPub 5.0 a text mining system to answer biological questions. Nucleic Acids Res. 2011;39:W450-4 pubmed publisher
    ..Finally, operations of the CoPub 5.0 Web service enable to implement the CoPub technology in bioinformatics workflows. CoPub 5.0 can be accessed through the CoPub portal ..
  6. Lokker C, Haynes R, Wilczynski N, McKibbon K, Walter S. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters. J Am Med Inform Assoc. 2011;18:652-9 pubmed publisher
    ..and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters...
  7. Richter R, Austin T. Using MeSH (medical subject headings) to enhance PubMed search strategies for evidence-based practice in physical therapy. Phys Ther. 2012;92:124-32 pubmed publisher
    ..controlled vocabulary thesaurus of indexing terms, is used to efficiently search MEDLINE, the largest component of PubMed. Using clinical questions, this report illustrates how search terms common to physical therapist practice do or do ..
  8. Névéol A, Wilbur W, Lu Z. Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics. 2011;27:3306-12 pubmed publisher
    ..We apply machine learning algorithms to sentences extracted from full-text articles in PubMed Central in order to automatically determine whether a given article contains a data deposition statement, and ..
  9. Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2012;40:D13-25 pubmed publisher
    ..NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, ..
  10. Li J, Lu Z. Systematic identification of pharmacogenomics information from clinical trials. J Biomed Inform. 2012;45:870-8 pubmed publisher
    ..This work has practical implications in enriching our existing knowledge on PGx gene-drug-disease relationships as well as suggesting crosslinks between and other PGx knowledge bases. ..
  11. Hakenberg J, Voronov D, Nguyên V, Liang S, Anwar S, Lumpkin B, et al. A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. J Biomed Inform. 2012;45:842-50 pubmed publisher
    ..We mine textual data from PubMed abstracts to discover such genotype-phenotype associations, focusing on SNPs that can be associated with ..
  12. Nourbakhsh E, Nugent R, Wang H, Cevik C, Nugent K. Medical literature searches: a comparison of PubMed and Google Scholar. Health Info Libr J. 2012;29:214-22 pubmed publisher
    ..We compared search results using PubMed and Google Scholar on four clinical questions and analysed these results with respect to article relevance and ..
  13. Waffenschmidt S, Janzen T, Hausner E, Kaiser T. Simple search techniques in PubMed are potentially suitable for evaluating the completeness of systematic reviews. J Clin Epidemiol. 2013;66:660-5 pubmed publisher
    ..Our aim was to determine whether PubMed's Related Citations (RelCits) and/or a simple-structured Boolean search (SSBS) are efficient and reliable search ..
  14. Wei C, Harris B, Li D, Berardini T, Huala E, Kao H, et al. Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford). 2012;2012:bas041 pubmed publisher
    ..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...
  15. Shariff S, Sontrop J, Haynes R, Iansavichus A, McKibbon K, Wilczynski N, et al. Impact of PubMed search filters on the retrieval of evidence by physicians. CMAJ. 2012;184:E184-90 pubmed publisher
    Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles...
  16. Sheets L, Gavino A, Callaghan F, Fontelo P. Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?. Appl Clin Inform. 2013;4:170-84 pubmed publisher
    ..This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in ..
  17. Roy S, Heinrich K, Phan V, Berry M, Homayouni R. Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. BMC Bioinformatics. 2011;12 Suppl 10:S19 pubmed publisher
    ..In addition, unlike motif searching approaches, LSI based approaches can reveal TFs that may indirectly regulate genes. ..
  18. Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr aryamontri A, Winter A, et al. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 2011;12 Suppl 8:S3 pubmed publisher
    ..was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times...
  19. Tsuruoka Y, Miwa M, Hamamoto K, Tsujii J, Ananiadou S. Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics. 2011;27:i111-9 pubmed publisher
    ..The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical ..
  20. Barbosa Silva A, Fontaine J, Donnard E, Stussi F, Ortega J, Andrade Navarro M. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011;12:435 pubmed publisher
    ..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-..
  21. Sayyah Ensan L, Faghankhani M, Javanbakht A, Ahmadi S, Baradaran H. To compare PubMed Clinical Queries and UpToDate in teaching information mastery to clinical residents: a crossover randomized controlled trial. PLoS ONE. 2011;6:e23487 pubmed publisher
    To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction...
  22. Thomas P, Starlinger J, Vowinkel A, Arzt S, Leser U. GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res. 2012;40:W585-91 pubmed publisher
    ..GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts...
  23. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011;27:1723-4 pubmed publisher
    ..of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images. The extensions can be downloaded from http://figuresearch.askhermes...
  24. Huang M, Névéol A, Lu Z. Recommending MeSH terms for annotating biomedical articles. J Am Med Inform Assoc. 2011;18:660-7 pubmed publisher
    ..All data sets are available at: ..
  25. Wang H, Ding Y, Tang J, Dong X, He B, Qiu J, et al. Finding complex biological relationships in recent PubMed articles using Bio-LDA. PLoS ONE. 2011;6:e17243 pubmed publisher
    ..This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing. ..
  26. Wei C, Kao H, Lu Z. PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 2013;41:W518-22 pubmed publisher
    ..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 ..
  27. Jourquin J, Duncan D, Shi Z, Zhang B. GLAD4U: deriving and prioritizing gene lists from PubMed literature. BMC Genomics. 2012;13 Suppl 8:S20 pubmed publisher
    ..genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists...
  28. Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C. pubmed2ensembl: a resource for mining the biological literature on genes. PLoS ONE. 2011;6:e24716 pubmed publisher, an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g...
  29. Kim S, Kim W, Wei C, Lu Z, Wilbur W. Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database (Oxford). 2012;2012:bas042 pubmed publisher
    ..Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. ..
  30. Agarwal S, Yu H, Kohane I. BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011;12:420 pubmed publisher
    ..million biomedical sentences from three resources: ?2 million full-text biomedical articles in Elsevier and the PubMed Central, as well as ?20 million abstracts in PubMed...
  31. Agoritsas T, Merglen A, Courvoisier D, Combescure C, Garin N, Perrier A, et al. Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews. J Med Internet Res. 2012;14:e85 pubmed publisher
    Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge...
  32. Fontelo P, Liu F. Finding translational science publications in MEDLINE/PubMed with translational science filters. Clin Transl Sci. 2011;4:455-9 pubmed publisher
    Translational Science Search (TSS; 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...
  33. Wang W, Haerian K, Salmasian H, Harpaz R, Chase H, Friedman C. A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations. AMIA Annu Symp Proc. 2011;2011:1464-70 pubmed
    ..determines whether a specific adverse event (AE) is caused by a specific drug based on the content of PubMed citations...
  34. Mendis K. Health informatics research in Australia: retrospective analysis using PubMed. Inform Prim Care. 2007;15:17-23 pubmed
    To obtain an overview of Australian health informatics (HI) research through a bibliometric analysis using PubMed. Australian HI publications from 1970 to 2005 were downloaded in Medline format using PubMed queries...
  35. Rossner M. The Journal of General Physiology on PubMed Central. J Gen Physiol. 2007;130:541 pubmed
  36. States D, Ade A, Wright Z, Bookvich A, Athey B. MiSearch adaptive pubMed search tool. Bioinformatics. 2009;25:974-6 pubmed publisher
    ..acquired during browsing and used to dynamically update a likelihood model that includes authorship, journal and PubMed indexing information...
  37. Tuttle B, von Isenburg M, Schardt C, Powers A. PubMed instruction for medical students: searching for a better way. Med Ref Serv Q. 2009;28:199-210 pubmed publisher
    In 2007, Duke University Medical Center Library instituted an interactive, online PubMed tutorial and quiz for medical students to replace an in-person lecture...
  38. Sintchenko V, Anthony S, Phan X, Lin F, Coiera E. A PubMed-wide associational study of infectious diseases. PLoS ONE. 2010;5:e9535 pubmed publisher
    ..A significant proportion of the more than 18 million manuscripts indexed in the PubMed database describe infectious disease syndromes and various infectious agents...
  39. Gerner M, Nenadic G, Bergman C. LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics. 2010;11:85 pubmed publisher
    ..system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers...
  40. Li J, Zhu X, Chen J. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol. 2009;5:e1000450 pubmed publisher
    ..Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular ..
  41. Sayers E, Barrett T, Benson D, Bryant S, Canese K, Chetvernin V, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009;37:D5-15 pubmed publisher
    ..NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, ..
  42. Nichols A. Sports medicine clinical trial research publications in academic medical journals between 1996 and 2005: an audit of the PubMed MEDLINE database. Br J Sports Med. 2008;42:909-21 pubmed
    To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and ..
  43. Schardt C, Adams M, Owens T, Keitz S, Fontelo P. Utilization of the PICO framework to improve searching PubMed for clinical questions. BMC Med Inform Decis Mak. 2007;7:16 pubmed
    ..was designed as a pilot study to measure the relevancy of search results using three different interfaces for the PubMed search system...
  44. Niu Y, Otasek D, Jurisica I. Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics. 2010;26:111-9 pubmed publisher
    ..evidence for approximately 60% of interactions when both proteins appear in at least one sentence in the PubMed abstract...
  45. Klaewsongkram J, Reantragoon R. Asthma research performance in Asia-Pacific: a bibliometric analysis by searching PubMed database. J Asthma. 2009;46:1013-20 pubmed publisher
    ..Asthma articles from Asia-Pacific countries published between 1998 and 2007 were retrieved from PubMed by searching MeSH for "asthma...
  46. Yu W, Yesupriya A, Wulf A, Qu J, Khoury M, Gwinn M. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. BMC Bioinformatics. 2007;8:436 pubmed this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data...
  47. Anders M, Evans D. Comparison of PubMed and Google Scholar literature searches. Respir Care. 2010;55:578-83 pubmed
    ..To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark...
  48. Uthman O, Uthman M. Geography of Africa biomedical publications: an analysis of 1996-2005 PubMed papers. Int J Health Geogr. 2007;6:46 pubmed
    ..and contribution of different Africa subregions and individual countries as represented by the articles indexed by PubMed between 1996 and 2005...
  49. Simon M, Hausner E, Klaus S, Dunton N. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface. BMC Med Res Methodol. 2010;10:76 pubmed publisher
    The identification of health services research in databases such as PubMed/Medline is a cumbersome task...
  50. Grüning B, Senger C, Erxleben A, Flemming S, Günther S. Compounds In Literature (CIL): screening for compounds and relatives in PubMed. Bioinformatics. 2011;27:1341-2 pubmed publisher
    ..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...
  51. Jelier R, Schuemie M, Roes P, van Mulligen E, Kors J. Literature-based concept profiles for gene annotation: the issue of weighting. Int J Med Inform. 2008;77:354-62 pubmed
    ..When larger amounts of texts were available for the generation of the concepts' vectors, the performance of the methods diverged considerably, with the uncertainty coefficient then outperforming the two other methods. ..
  52. Ananiadou S, Pyysalo S, Tsujii J, Kell D. Event extraction for systems biology by text mining the literature. Trends Biotechnol. 2010;28:381-90 pubmed publisher
    ..The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states. ..
  53. Hopewell S, Dutton S, Yu L, Chan A, Altman D. The quality of reports of randomised trials in 2000 and 2006: comparative study of articles indexed in PubMed. BMJ. 2010;340:c723 pubmed publisher
    To 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 ..