bibliographic databases


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.

Top Publications

  1. Tafuri G, Trotta F, Leufkens H, Martini N, Sagliocca L, Traversa G. 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 disease. Eur J Clin Pharmacol. 2009;65:209-16 pubmed publisher
    ..Regulatory agencies and ethical committees should cope with this issue for ethical reasons to avoid unnecessary trial replication. ..
  2. Löhönen J, Isohanni M, Nieminen P, Miettunen J. A guide for medical information searches of bibliographic databases - psychiatric research as an example. Int J Circumpolar Health. 2009;68:394-404 pubmed
    Information 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 ..
  3. Gonzalez Sagrado M, Luis Román D, Conde Vicente R, Izaola O, Aller R, Perez Castrillon J. [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]. Nutr Hosp. 2008;23:111-8 pubmed
  4. Löhönen J, Isohanni M, Nieminen P, Miettunen J. Coverage of the bibliographic databases in mental health research. Nord J Psychiatry. 2010;64:181-8 pubmed publisher
    Electronic bibliographic databases are important tools when searching for medical information. The selected databases have an important effect on the potential results achieved...
  5. Vanhecke T, Barnes M, Zimmerman J, Shoichet S. PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines. Comput Biol Med. 2007;37:1252-8 pubmed
    ..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. ..
  6. Xia J, Wright J, Adams C. Five large Chinese biomedical bibliographic databases: accessibility and coverage. Health Info Libr J. 2008;25:55-61 pubmed publisher
    ..Searches in all databases benefit from the use of simplified Chinese and all provide links to full text articles. Less than 6% of the 2500 journals in the five databases were listed as being indexed for MEDLINE. ..
  7. Kostoff R. Validating discovery in literature-based discovery. J Biomed Inform. 2007;40:448-50; author reply 450-2 pubmed
  8. Chen D, Muller H, Sternberg P. Automatic document classification of biological literature. BMC Bioinformatics. 2006;7:370 pubmed
    ..We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. ..
  9. Cohen K, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008;4:e20 pubmed publisher

More Information


  1. Rossner M, Van Epps H, Hill E. Show me the data. J Cell Biol. 2007;179:1091-2 pubmed
  2. Rossner M, Van Epps H, Hill E. Show me the data. J Exp Med. 2007;204:3052-3 pubmed
  3. Kostoff R, Johnson D, Rio J, Bloomfield L, Shlesinger M, Malpohl G, et al. Duplicate publication and 'paper inflation' in the Fractals literature. Sci Eng Ethics. 2006;12:543-54 pubmed
    ..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. ..
  4. Caporaso J, Baumgartner W, Randolph D, Cohen K, Hunter L. MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics. 2007;23:1862-5 pubmed
    ..Implementations, source code and unit tests are available in Python, Perl and Java. MutationFinder can be used as a stand-alone script, or imported by other applications. ..
  5. Errami M, Wren J, Hicks J, Garner H. eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. Nucleic Acids Res. 2007;35:W12-5 pubmed
    ..These services are freely accessible through the Internet at, where users can upload a file or paste text such as an abstract into the browser interface. ..
  6. Al Hajeri A, Al Sayyad J, Eisinga A. Handsearching the EMHJ for reports of randomized controlled trials by U.K. Cochrane Centre (Bahrain). East Mediterr Health J. 2006;12 Suppl 2:S253-7 pubmed
    ..Reports identified were sent to the UK Cochrane Centre for verification and publication in The Cochrane Central Register of Controlled Trials (CENTRAL). ..
  7. Shultz M. Comparing test searches in PubMed and Google Scholar. J Med Libr Assoc. 2007;95:442-5 pubmed
  8. Zhou W, Torvik V, Smalheiser N. ADAM: another database of abbreviations in MEDLINE. Bioinformatics. 2006;22:2813-8 pubmed
    ..A free, public query interface to ADAM is available at, and the entire database can be downloaded as a text file. ..
  9. Zorzetto R, Razzouk D, Dubugras M, Gerolin J, Schor N, Guimaraes J, et al. The scientific production in health and biological sciences of the top 20 Brazilian universities. Braz J Med Biol Res. 2006;39:1513-20 pubmed
    ..7% of the papers in these areas and are strongly concentrated in the Southern part of the country, mainly in São Paulo State. ..
  10. Grimes G, Wen T, Mewissen M, Baxter R, Moodie S, Beattie J, et al. PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature. Bioinformatics. 2006;22:2055-7 pubmed
    ..PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. PDQ Wizard is freely available from ..
  11. Hearst M, Divoli A, Guturu H, Ksikes A, Nakov P, Wooldridge M, et al. BioText Search Engine: beyond abstract search. Bioinformatics. 2007;23:2196-7 pubmed
    ..The interface is carefully designed according to usability principles and techniques. The search engine is a work in progress, and more functionality will be added over time. ..
  12. Falagas M, Giannopoulou K, Issaris E, Spanos A. World databases of summaries of articles in the biomedical fields. Arch Intern Med. 2007;167:1204-6 pubmed
  13. Gorecki C, Brown J, Briggs M, Nixon J. Evaluation of five search strategies in retrieving qualitative patient-reported electronic data on the impact of pressure ulcers on quality of life. J Adv Nurs. 2010;66:645-52 pubmed publisher
    ..Accurate indexing of subject-specific outcomes and methodology used in electronic databases and publications is also needed. ..
  14. Jørgensen H, Larsen B, Ingwersen P, Rehfeld J. [Research activity in clinical biochemistry]. Ugeskr Laeger. 2008;170:2798-802 pubmed
    ..Both the number of papers and the number of citations were higher for Clinical Biochemistry than for the control group. The difference was most pronounced among professors. ..
  15. Lambers Heerspink H, Perkovic V, de Zeeuw D. Renal and cardio-protective effects of direct renin inhibition: a systematic literature review. J Hypertens. 2009;27:2321-31 pubmed publisher
    ..Results of ongoing hard outcome trials are awaited to definitively assess the renal and cardio-protective effects of these agents. ..
  16. McCabe M. Fatigue in children with long-term conditions: an evolutionary concept analysis. J Adv Nurs. 2009;65:1735-45 pubmed publisher
    ..Ongoing study as a means to refine our understanding of the concept could potentially lead to important contributions to clinical care of children with long-term conditions. ..
  17. Foroughi N, Smith R, Vanwanseele B. The association of external knee adduction moment with biomechanical variables in osteoarthritis: a systematic review. Knee. 2009;16:303-9 pubmed publisher
    ..These variables should be taken into considerations when developing therapeutic interventions for individuals suffering from knee OA. ..
  18. Tomizawa Y. [Use of cyber library and digital tools are crucial for academic surgeons]. Kyobu Geka. 2010;63:983-7 pubmed
    ..The use of cyber library and commercially available computer software is useful in saving time and effort. ..
  19. Bryant J, Baxter L, Hird S. Non-occupational postexposure prophylaxis for HIV: a systematic review. Health Technol Assess. 2009;13:iii, ix-x, 1-60 pubmed publisher
  20. Yetisgen Yildiz M, Pratt W. A new evaluation methodology for literature-based discovery systems. J Biomed Inform. 2009;42:633-43 pubmed publisher
    ..This evaluation methodology should help other researchers compare approaches, make informed algorithm choices, and ultimately help to improve the performance of LBD systems overall. ..
  21. Murphy M, Quinn S, Young J, Parkin P, Taylor B. Increasing incidence of ALS in Canterbury, New Zealand: a 22-year study. Neurology. 2008;71:1889-95 pubmed publisher
    ..The increasing incidence is not explained by aging of the population. ..
  22. Stevenson M, Guo Y, Gaizauskas R, Martinez D. Disambiguation of biomedical text using diverse sources of information. BMC Bioinformatics. 2008;9 Suppl 11:S7 pubmed publisher
    ..Disambiguation of biomedical terms benefits from the use of information from a variety of sources. In particular, MeSH terms have proved to be useful and should be used if available. ..
  23. Zhuo X, Wang Y, Zhuo W, Zhang X. Is the application of prostaglandin E1 effective for the treatment of sudden hearing loss? An evidence-based meta-analysis. J Int Med Res. 2008;36:467-70 pubmed
    ..The pooled odds ratio was 1.95 (95% confidence interval: 1.53, 2.50) and the test for overall effect (Z-value) was 5.31 (P < 0.00001), suggesting that PGE(1) is an effective and promising strategy for the treatment of SHL...
  24. Aerts R. Digital identifiers work for articles, so why not for authors?. Nature. 2008;453:979 pubmed publisher
  25. Qin H, Liu B, Shi T, Liu Y, Sun Y, Ma Y. Tumour necrosis factor-alpha polymorphisms and hepatocellular carcinoma: a meta-analysis. J Int Med Res. 2010;38:760-8 pubmed
    ..When comparing with hepatitis B virus infection cases, no statistical association was found. This meta-analysis suggests that TNFA -308GG gene polymorphism is associated with a modest decrease in the risk of HCC. ..
  26. Tomizawa Y. [Ichushi, Japanese medical bibliography]. Kyobu Geka. 2010;63:585-9 pubmed
    ..The form was changed from booklet to CD-ROM, and then through the internet. Recently, the database covers medicine, nursing, dentistry, and veterinary medicine. ..
  27. Cady R, Maizels M, Reeves D, Levinson D, Evans J. Predictors of adherence to triptans: factors of sustained vs lapsed users. Headache. 2009;49:386-94 pubmed publisher
    ..The findings suggest that lapsed users may not be receiving optimal treatment, and that if their past response to triptans was a consequence of inadequate education, they may benefit from additional education on proper use of triptans. ..
  28. Errami M, Sun Z, Long T, George A, Garner H. Deja vu: a database of highly similar citations in the scientific literature. Nucleic Acids Res. 2009;37:D921-4 pubmed publisher
    ..The Déjà vu database is freely accessible at The tool eTBLAST is also freely available at ..
  29. Tsuruoka Y, Tsujii J, Ananiadou S. Accelerating the annotation of sparse named entities by dynamic sentence selection. BMC Bioinformatics. 2008;9 Suppl 11:S8 pubmed publisher
    ..The cost reduction achieved by the framework could be drastic when the target named entities are sparse. ..
  30. Beaudreuil J, Nizard R, Thomas T, Peyre M, Liotard J, Boileau P, et al. Contribution of clinical tests to the diagnosis of rotator cuff disease: a systematic literature review. Joint Bone Spine. 2009;76:15-9 pubmed publisher
    ..To evaluate the diagnostic performance of clinical tests for degenerative rotator cuff disease, based on a systematic literature review...
  31. Schmid H, Schiffl H, Lederer S. Pharmacotherapy of end-stage renal disease. Expert Opin Pharmacother. 2010;11:597-613 pubmed publisher
    ..Individualized and tailor-made pharmacological management of the ESRD patient remains a challenge for the future. ..
  32. Roche B, Larroumets G, Dejax C, Kwiatkowsi F, Desbiez F, Thieblot P, et al. Epidemiology, clinical presentation, treatment and prognosis of a regional series of 26 anaplastic thyroid carcinomas (ATC). Comparison with the literature. Ann Endocrinol (Paris). 2010;71:38-45 pubmed publisher
    ..In a multivariate analysis only age above 75, followed by node invasion, capsular invasion, and finally female gender are factors of poor prognosis. ..
  33. Assari S. Domestic versus international Iranian transplantation publication: a comparative study. Ann Transplant. 2009;14:58-61 pubmed
    ..So, domestic scientific databases should be regarded as a pool of valuable information, and should be introduced to researchers of other countries, such as Middle East Society for Organ Transplantation region. ..
  34. Smith T, Hing C. Is a tourniquet beneficial in total knee replacement surgery? A meta-analysis and systematic review. Knee. 2010;17:141-7 pubmed publisher
    ..In conclusion, this systematic review has found that there is no advantage to using a tourniquet in knee replacement surgery for reduction of transfusion requirements. ..
  35. Willis N, Pascual J. Evidence-based nephrology: the Cochrane Renal Review Group. Nefrologia. 2008;28 Suppl 2:46-50 pubmed
  36. Tess B, Furuie S, Castro R, Barreto M, Nobre M. Assessing the scientific research productivity of a Brazilian healthcare institution: a case study at the Heart Institute of São Paulo, Brazil. Clinics (Sao Paulo). 2009;64:571-6 pubmed
    ..The institutional impact factor of articles indexed in the Web of Science may serve as a measure by which to assess and review the scientific productivity of a research institution. ..
  37. Gaida J, Ashe M, Bass S, Cook J. Is adiposity an under-recognized risk factor for tendinopathy? A systematic review. Arthritis Rheum. 2009;61:840-9 pubmed publisher
    ..Further research is required to determine if reducing adiposity will reduce the risk of tendon injury or improve the results of treatment. ..
  38. Thanacoody R. Extracorporeal elimination in acute valproic acid poisoning. Clin Toxicol (Phila). 2009;47:609-16 pubmed publisher
    ..Controlled, randomized trials are required to better characterize the effect of extracorporeal treatment on clinical outcome. ..
  39. Ogourtsova T, Korner Bitensky N, Ptito A. Contribution of the superior colliculi to post-stroke unilateral spatial neglect and recovery. Neuropsychologia. 2010;48:2407-16 pubmed publisher
    ..Further exploration of the mechanisms involved and their impact on USN in human subjects will help develop theoretically based intervention strategies tailored to USN type. ..
  40. Allan G, Korownyk C, Tan A, Hindle H, Kung L, Manca D. Developing an integrated evidence-based medicine curriculum for family medicine residency at the University of Alberta. Acad Med. 2008;83:581-7 pubmed publisher
    ..The first two years of the curriculum have yielded positive feedback from faculty and statistically significant improvement in multiple areas of residents' opinions of the curriculum and comfort with evidence-based practice. ..
  41. Trujillo Martín M, Serrano Aguilar P, Monton Alvarez F, Carrillo Fumero R. Effectiveness and safety of treatments for degenerative ataxias: a systematic review. Mov Disord. 2009;24:1111-24 pubmed publisher
    ..No valid information on the actual value of physical rehabilitation and psychological support as treatments for DA is available. Further investigations with improved trial designs are necessary. ..
  42. Gavaza P, Rascati K, Oladapo A, Khoza S. The state of health economic evaluation research in Nigeria: a systematic review. Pharmacoeconomics. 2010;28:539-53 pubmed publisher
    ..More and better quality health economic research in Nigeria is warranted. ..
  43. Xu Y, Wang Z, Lei Y, Zhao Y, Xue Y. MBA: a literature mining system for extracting biomedical abbreviations. BMC Bioinformatics. 2009;10:14 pubmed publisher
    ..g., <CNS1, cyclophilin seven suppressor>), but also non-acronym-type abbreviations (e.g., <Fas, CD95>). ..
  44. Smith M, Hopkins D, Peveler R, Holt R, Woodward M, Ismail K. First- v. second-generation antipsychotics and risk for diabetes in schizophrenia: systematic review and meta-analysis. Br J Psychiatry. 2008;192:406-11 pubmed publisher
    ..Methodological limitations were found in most studies, leading to heterogeneity and difficulty interpreting data. Regardless of type of antipsychotic, screening for diabetes in all people with schizophrenia should be routine. ..
  45. Citrome L, Moss S, Graf C. How to search and harvest the medical literature: let the citations come to you, and how to proceed when they do. Int J Clin Pract. 2009;63:1565-70 pubmed publisher
    ..Clinicians and researchers can take advantage of this and efficiently harvest the medical literature with a modest investment of time. ..
  46. Rogers G, Elston J, Garside R, Roome C, Taylor R, Younger P, et al. The harmful health effects of recreational ecstasy: a systematic review of observational evidence. Health Technol Assess. 2009;13:iii-iv, ix-xii, 1-315 pubmed publisher
    ..Ecstasy is associated with a range of acute harms but appears to be a rare cause of death in isolation. ..
  47. Gulis G, Eriksen M, Aro A. Public health research in Denmark in the years 1995--2005. Scand J Public Health. 2010;38:104-7 pubmed publisher
    ..Overall, public health research in Denmark seems to contribute around 4.8%-6.5% of the total amount of health research. Public health research has a relatively low share of overall health research in Denmark. ..
  48. Abi Haidar A, Kaur J, Maguitman A, Radivojac P, Rechtsteiner A, Verspoor K, et al. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome Biol. 2008;9 Suppl 2:S11 pubmed publisher
    ..In full-text problems, the expansion of word features with word proximity networks is shown to be useful, although the need for some improvements is discussed. ..
  49. Macfarlane A, Prasad G, Chan V, Brull R. Does regional anesthesia improve outcome after total knee arthroplasty?. Clin Orthop Relat Res. 2009;467:2379-402 pubmed publisher
    ..Length of stay may be reduced and rehabilitation facilitated for patients undergoing regional anesthesia and analgesia for TKA. ..
  50. Jankovic M, Kaufmann M, Kindler C. Active research fields in anesthesia: a document co-citation analysis of the anesthetic literature. Anesth Analg. 2008;106:1524-33, table of contents pubmed publisher
    ..Using co-citation analysis, we identified distinct homogenous clusters of highly cited documents representing 46 active current anesthetic research fields and determined multiple nets of knowledge among them. ..
  51. Yoshii A, Plaut D, McGraw K, Anderson M, Wellik K. Analysis of the reporting of search strategies in Cochrane systematic reviews. J Med Libr Assoc. 2009;97:21-9 pubmed publisher
    ..The 65 reviews represented 41 different Cochrane review groups. The instructions from the Cochrane Handbook for reporting search strategies are not being consistently employed by groups producing Cochrane reviews. ..
  52. Foo J. The retrospective analysis of bibliographical trends for nine biomedical engineering journals from 1999 to 2007. Ann Biomed Eng. 2009;37:1474-81 pubmed publisher
    ..The retrospective impacts of these influences on the nine selected journals over the 9-year period were also discussed in this study. ..
  53. Greene S, Wood D, Gawarammana I, Warren Gash C, Drake N, Jones A, et al. Improvement in the management of acutely poisoned patients using an electronic database, prospective audit and targeted educational intervention. Postgrad Med J. 2008;84:603-8 pubmed publisher
    ..This process has led to significant improvements in the clinical care of acutely poisoned patients presenting to the ED. ..