The new-look of PubMed: A brief description of the changes in PubMed

Authors

  • Fabio Frisone Department of Cognitive Sciences, Psychology, Educational and Cultural Studies (COSPECS), University of Messina - 2 CRISCAT (International Research Center for Theoretical and Applied Cognitive Sciences) University of Messina and Universitary Consortium of Eastern Mediterranean, Noto (CUMO) https://orcid.org/0000-0002-1766-831X
  • Rosaria Micali Library System, University of Messina

DOI:

https://doi.org/10.6092/2282-1619/mjcp-2534

Keywords:

Pubmed, Scientific Information, Web Retrieval, Innovation, Technology, Clinical Psychology.

Abstract

The advancement of technology has made it possible to obtain discrete results in terms of scientific information.  Among the many innovations made recently, there is the possibility of accessing the changes and improvements offered by the new updated PubMed.  This brief description aims at highlighting the main innovations operated by PubMed to make the field of scientific information more practical and reachable by everyone.

Author Biography

  • Fabio Frisone, Department of Cognitive Sciences, Psychology, Educational and Cultural Studies (COSPECS), University of Messina - 2 CRISCAT (International Research Center for Theoretical and Applied Cognitive Sciences) University of Messina and Universitary Consortium of Eastern Mediterranean, Noto (CUMO)
    University of Messina, PhD St.

References

AlRyalat, S. A. S., Malkawi, L. W., & Momani, S. M. (2019). Comparing bibliometric analysis using PubMed, Scopus, and Web of Science databases. JoVE (Journal of Visualized Experiments), (152), e58494.

https://doi.org/10.3791/58494

Berardi, M., Lapi, M., Leo, P., Malerba, D., Marinelli, C., & Scioscia, G. (2004, September). A data mining approach to PubMed query refinement. In Proceedings. 15th International Workshop on Database and Expert Systems Applications, 2004. (pp. 401-405). IEEE.

https://doi.org/10.1109/DEXA.2004.1333507

Bernacki, J., Błażejczyk, I., Indyka-Piasecka, A., Kopel, M., Kukla, E., & Trawiński, B. (2016, March). Responsive web design: testing usability of mobile web applications. In Asian Conference on Intelligent Information and Database Systems (pp. 257-269). Springer, Berlin, Heidelberg.

https://doi.org/10.1007/978-3-662-49381-6_25

Bhaskar, P., Buzzi, M., Geraci, F., & Pellegrini, M. (2015, September). From literature to knowledge: Exploiting pubmed to answer biomedical questions in natural language. In International Conference on Information Technology in Bio-and Medical Informatics (pp. 3-15). Springer, Cham.

https://doi.org/10.1007/978-3-319-22741-2_1

Blom‐Hoffman, J., Okun, B. F., Lifter, K., Blashfield, R., Crowley, S. L., Goodyear, R. K., ... & Winfrey, L. L. (2004). Voices of the five doctoral training councils in psychology: Seeking common ground on Combined‐Integrated doctoral training in psychology. Journal of clinical psychology, 60(9), 957-967.

https://doi.org/10.1002/jclp.20029

Caelleigh, A. S. (2000). PubMed Central and the new publishing landscape: shifts and tradeoffs.

https://doi.org/10.1097/00001888-200001000-00004

Canese K. (2019). The New PubMed Updated: Homepage, User Guide, My NCBI Alerts and Collections, and More. NLM Technical Bullettin. Sep-Oct;(430):e5.

Cortegiani, A., Manca, A., & Giarratano, A. (2020). Predatory journals and conferences: why fake counts. Current Opinion in Anesthesiology, 33(2), 192-197.

https://doi.org/10.1097/ACO.0000000000000829

Cortegiani, A., Sanfilippo, F., Tramarin, J., & Giarratano, A. (2019). Predatory open-access publishing in critical care medicine. Journal of Critical Care, 50, 247-249.

https://doi.org/10.1016/j.jcrc.2018.12.016

Costantino, G., Montano, N., & Casazza, G. (2015). When should we change our clinical practice based on the results of a clinical study? Searching for evidence: PICOS and PubMed. Internal and emergency medicine, 10(4), 525-527.

https://doi.org/10.1007/s11739-015-1225-5

Damarell, R. A., Lewis, S., Trenerry, C., & Tieman, J. J. (2020). Integrated Care Search: development and validation of a PubMed search filter for retrieving the integrated care research evidence. BMC medical research methodology, 20(1), 12.

https://doi.org/10.1186/s12874-020-0901-y

Dogan, R. I., Murray, G. C., Névéol, A., & Lu, Z. (2009). Understanding PubMed user search behavior through log analysis. Database, 2009, bap018.

https://doi.org/10.1093/database/bap018

Dosier, C. (1947). Report of roundtable on internship and training of clinical psychologists. Journal of Clinical Psychology.

https://doi.org/10.1002/1097-4679(194704)3:2<184::AID-JCLP2270030212>3.0.CO;2-N

Duffy, S., de Kock, S., Misso, K., Noake, C., Ross, J., & Stirk, L. (2016). Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid. Journal of the Medical Library Association: JMLA, 104(4), 309.

https://doi.org/10.3163/1536-5050.104.4.011

Falagas, M. E., Pitsouni, E. I., Malietzis, G. A., & Pappas, G. (2008). Comparison of PubMed, Scopus, web of science, and Google scholar: strengths and weaknesses. The FASEB journal, 22(2), 338-342.

https://doi.org/10.1096/fj.07-9492LSF

Fiorini N, Canese K, Bryzgunov R, et al. (2018). PubMed Labs: an experimental system for improving biomedical literature search. Database (Oxford).

https://doi.org/10.1093/database/bay094

Fiorini, N., Canese, K., Starchenko, G., Kireev, E., Kim, W., Miller, V., ... & Ostell, J. (2018). Best match: new relevance search for PubMed. PLoS biology, 16(8), e2005343.

https://doi.org/10.1371/journal.pbio.2005343

Fiorini, N., Leaman, R., Lipman, D. J., & Lu, Z. (2018). How user intelligence is improving PubMed. Nature biotechnology, 36(10), 937-945.

https://doi.org/10.1038/nbt.4267

Fiorini, N., Lipman, D. J., & Lu, Z. (2017). Cutting edge: towards PubMed 2.0. Elife, 6, e28801.

https://doi.org/10.7554/eLife.28801

Fontaine, J. F., Barbosa-Silva, A., Schaefer, M., Huska, M. R., Muro, E. M., & Andrade-Navarro, M. A. (2009). MedlineRanker: flexible ranking of biomedical literature. Nucleic acids research, 37(suppl_2), W141-W146.

https://doi.org/10.1093/nar/gkp353

Frandsen, T. F., Eriksen, M. B., Hammer, D. M. G., & Christensen, J. B. (2019). PubMed coverage varied across specialties and over time: a large-scale study of included studies in Cochrane reviews. Journal of clinical epidemiology, 112, 59-66.

https://doi.org/10.1016/j.jclinepi.2019.04.015

Frisone, F. (2018). Most cited articles in Clinical Psychology. MEDITERRANEAN JOURNAL OF CLINICAL PSYCHOLOGY, 6(1).

https://doi.org/10.6092/2282-1619/2018.6.1907

Gargiulo, F., Silvestri, S., & Ciampi, M. (2017, July). A big data architecture for knowledge discovery in PubMed articles. In 2017 IEEE Symposium on Computers and Communications (ISCC) (pp. 82-87). IEEE.

https://doi.org/10.1109/ISCC.2017.8024509

Giglia, E. (2007). Beyond Pubmed-other free access biomedical databases. Europa medicophysica.

Giglia, E. (2009). New year, new PubMed. European journal of physical and rehabilitation medicine, 45(1), 155-159.

Giglia, E. (2011). PubMed in progress: latest changes in MeSH and MyNCBI. European Journal of Physical and Rehabilitation Medicine, 47(3), 525-528.

Gusenbauer, M., & Haddaway, N. R. (2020). Which academic search systems are suitable for systematic reviews or meta‐analyses? Evaluating retrieval qualities of Google Scholar, PubMed, and 26 other resources. Research synthesis methods, 11(2), 181-217.

https://doi.org/10.1002/jrsm.1378

Hogan Smith, K. (2018). Review of PubMed Health. Journal of Consumer Health on the Internet, 22(1), 80-87.

https://doi.org/10.1080/15398285.2018.1415594

Horne, R. (2006). Implications for Asthma Treatment Compliance, Adherence, and Concordance. Chest, 130, 65-72.

https://doi.org/10.1378/chest.130.1_suppl.65S

Huh, S. (2016). What is the meaning of becoming PubMed Central journal?. Korean Journal of Medical Education, 28(3), 265.

https://doi.org/10.3946/kjme.2016.38

Hunter, L., & Cohen, K. B. (2006). Biomedical language processing: what's beyond PubMed?. Molecular cell, 21(5), 589-594.

https://doi.org/10.1016/j.molcel.2006.02.012

Hussain, A., & Mkpojiogu, E. O. (2015). The effect of responsive web design on the user experience with laptop and smartphone devices. Jurnal Teknologi, 77(4), 41-47.

https://doi.org/10.11113/jt.v77.6041

Islamaj Dogan, R., Murray, G. C., Névéol, A., & Lu, Z. (2009). Understanding PubMed® user search behavior through log analysis. Database, 2009.

https://doi.org/10.1093/database/bap018

Jeong, G. H., & Huh, S. (2017). Bibliometric and content analysis of medical articles in the PubMed database published by North Korean authors from 1997 to July 2017. Sci Ed, 4(2), 70-75.

https://doi.org/10.6087/kcse.98

Kang, S. R., & Satterfield, D. (2019). Visual Identity Design for Responsive Web. In Advanced Methodologies and Technologies in Network Architecture, Mobile Computing, and Data Analytics (pp. 1828-1836). IGI Global.

https://doi.org/10.4018/978-1-5225-7598-6.ch135

Kumar, A. (2020). Medline [R], PubMed, PubMed Central.... Let's try to decipher. Journal of Indian Society of Periodontology, 24(3), 187-187.

Lanera, C., Berchialla, P., Sharma, A., Minto, C., Gregori, D., & Baldi, I. (2019). Screening PubMed abstracts: is class imbalance always a challenge to machine learning?. Systematic Reviews, 8(1), 317.

https://doi.org/10.1186/s13643-019-1245-8

Levenson, R. W. (2017). Clinical psychology training: Accreditation and beyond. Annual review of clinical psychology, 13, 1-22.

https://doi.org/10.1146/annurev-clinpsy-021815-093559

Lu, Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature. Database, 2011.

https://doi.org/10.1093/database/baq036

Lu, Z., Wilbur, W. J., McEntyre, J. R., Iskhakov, A., & Szilagyi, L. (2009). Finding query suggestions for PubMed. In AMIA Annual Symposium Proceedings (Vol. 2009, p. 396). American Medical Informatics Association.

Manca, A., Cugusi, L., Dvir, Z., & Deriu, F. (2017). PubMed should raise the bar for journal inclusion. The Lancet, 390(10096), 734-735.

https://doi.org/10.1016/S0140-6736(17)31943-8

Manca, A., Moher, D., Cugusi, L., Dvir, Z., & Deriu, F. (2018). How predatory journals leak into PubMed. CMAJ, 190(35), E1042-E1045.

https://doi.org/10.1503/cmaj.180154

McFall, R. M. (2006). Doctoral training in clinical psychology. Annu. Rev. Clin. Psychol., 2, 21-49.

https://doi.org/10.1146/annurev.clinpsy.2.022305.095245

Merlo, E. M. (2018). Index of scientific production during the 5 years of the MJCP. MEDITERRANEAN JOURNAL OF CLINICAL PSYCHOLOGY, 6(1).

https://doi.org/10.6092/2282-1619/2018.6.1907

Miah, S., Fung, V., Pang, K., & Begum, H. (2017). Curing ‘PubMed fever’. The Clinical Teacher, 14(2), 150-150.

https://doi.org/10.1111/tct.12610

Morshed, T., & Hayden, S. (2020). Google Versus PubMed: Comparison of Google and PubMed’s Search Tools for Answering Clinical Questions in the Emergency Department. Annals of Emergency Medicine, 75(3), 408-415.

https://doi.org/10.1016/j.annemergmed.2019.07.003

Phunkaew, T., Phandan, C., & Wongwatkit, C. (2019, October). Design and Evaluation of Interactive Learning Story and User Interface Prototyping for Mobile Responsive Learning Application. In 2019 4th International Conference on Information Technology (InCIT) (pp. 132-137). IEEE.

https://doi.org/10.1109/INCIT.2019.8912103

Plikus, M. V., Zhang, Z., & Chuong, C. M. (2006). PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm. BMC bioinformatics, 7(1), 424.

https://doi.org/10.1186/1471-2105-7-424

Rogers, J. R., Mills, H., Grossman, L. V., Goldstein, A., & Weng, C. (2020). Understanding the nature and scope of clinical research commentaries in PubMed. Journal of the American Medical Informatics Association, 27(3), 449-456.

https://doi.org/10.1093/jamia/ocz209

Settineri, S. (2018). “First division” and “Second division” Sciences. Mediterranean Journal of Clinical Psychology, 6(1).

https://doi.org/10.6092/2282-1619/2018.6.1842

Settineri, S., & Femminò, N. (2019). Science Communication in Clinical Psychology. Mediterranean Journal of Clinical Psychology, 7(1).

https://doi.org/10.6092/2282-1619/2019.7.2142

Settineri, S., Frisone, F., Alibrandi, A., & Merlo, E. M. (2019). Emotional suppression and oneiric expression in psychosomatic disorders: early manifestations in emerging adulthood and young patients. Frontiers in psychology, 10, 1897. https://doi.org/10.3389/fpsyg.2019.01897

Settineri, S., Frisone, F., Alibrandi, A., Pino, G., Lupo, N. J., & Merlo, E. M. (2018). Psychological Types and Learning Styles. Mediterranean Journal of Clinical Psychology, 6(3). https://doi.org/10.6092/2282-1619/2018.6.2005

Settineri, S., Frisone, F., Merlo, E. M., Geraci, D., & Martino, G. (2019). Compliance, adherence, concordance, empowerment, and self-management: five words to manifest a relational maladjustment in diabetes. Journal of multidisciplinary healthcare, 12, 299.

https://doi.org/10.2147/JMDH.S193752

Settineri, S., Merlo E. M., (2019). MJCP and Clinical Psychology. Mediterranean Journal of Clinical Psychology, 7(3).

https://doi.org/10.6092/2282-1619/2019.7.2346

Shanman, R. (2017). Phrase truncation in PubMed searches. Journal of the Medical Library Association: JMLA, 105(4), 404.

https://doi.org/10.5195/JMLA.2017.252

Shashikiran, N. (2016). MEDLINE, pubmed, and pubmed central®: Analogous or dissimilar. Journal of the Indian Society of Pedodontics and Preventive Dentistry, 34(3).

https://doi.org/10.4103/0970-4388.186748

Sperandeo, R., Messina, G., Iennaco, D., Sessa, F., Russo, V., Polito, R., ... & Mosca, L. (2019). What does personality mean in the context of mental health? A topic modeling approach based on abstracts published in PubMed over the last 5 years. Frontiers in psychiatry, 10.

https://doi.org/10.3389/fpsyt.2019.00938

States, D. J., Ade, A. S., Wright, Z. C., Bookvich, A. V., & Athey, B. D. (2009). MiSearch adaptive pubMed search tool. Bioinformatics, 25(7), 974-976.

https://doi.org/10.1093/bioinformatics/btn033

Subić, N., Krunić, T., & Gemović, B. (2014). Responsive web design–Are we ready for the new age. Online Journal of Applied Knowledge Management, 2(1), 93-103.

Topper, L., & Boehr, D. (2018). Publishing trends of journals with manuscripts in PubMed Central: changes from 2008–2009 to 2015–2016. Journal of the Medical Library Association: JMLA, 106(4), 445.

https://doi.org/10.5195/JMLA.2018.457

Tummers, M., van Hoorn, R., Levering, C., Booth, A., van der Wilt, G. J., & Kievit, W. (2019). Optimal search strategies for identifying moderators and predictors of treatment effects in PubMed. Health Information & Libraries Journal, 36(4), 318-340.

https://doi.org/10.1111/hir.12230

Turner, J. R. (2016). Pubmed, pubmed central, and impact factor. Cellular and Molecular Gastroenterology and Hepatology, 2(5), 537.

https://doi.org/10.1016/j.jcmgh.2016.07.004

Wanner, A., & Baumann, N. (2019). Design and implementation of a tool for conversion of search strategies between PubMed and Ovid MEDLINE. Research synthesis methods, 10(2), 154-160.

https://doi.org/10.1002/jrsm.1314

Wildgaard, L. E., & Lund, H. (2016). Advancing PubMed? A comparison of third-party PubMed/Medline tools. Library Hi Tech.

https://doi.org/10.1108/LHT-06-2016-0066

Williamson, P. O., & Minter, C. I. (2019). Exploring PubMed as a reliable resource for scholarly communications services. Journal of the Medical Library Association: JMLA, 107(1), 16.

https://doi.org/10.5195/JMLA.2019.433

Sitography

National Library of Medicine Technical Bulletin. (n. d.). An Updated PubMed Is on Its Way.

https://www.nlm.nih.gov/pubs/techbull/ma19/ma19_pubmed_update.html

National Library of Medicine. (n. d.). A New PubMed: Highlights for Information Professionals.

https://www.nlm.nih.gov/oet/ed/pubmed/events/2019_09.html.

Downloads

Published

13-08-2020

Issue

Vol. 8 No. 2 (2020)

Section

Reports

License

Creative Commons License Articles and conference papers published in Mediterranean Journal of Clinical Psychology are distributed under the terms and conditions of a Creative Commons Attribution 4.0 Unported License. Correspondingly, authors who publish with this journal agree to the following terms:

    1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.

    1. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.

  1. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).