PubMed and beyond: a survey of web tools for searching biomedical literature.
The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.
National Center for Biotechnology Information (NCBI), National Library of Medicine, Bethesda, MD 20894, USA. zhiyong.lu@nih.gov
Zhiyong
Z
Lu
D035843:Biomedical Research; D057225:Data Mining / Q000379:methods*; D003628:Database Management Systems; D020407:Internet; D039781:PubMed; D012984:Software
AMIA Annu Symp Proc. 2006;:923
17238542
Database (Oxford). 2009;2009:bap018
20157491
BMC Bioinformatics. 2007 Oct 30;8:423
17971238
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W774-8
15980583
EMBO Rep. 2010 May;11(5):345-9
20428107
Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16
19910364
Genome Biol. 2005;6(9):R80
16168087
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W12-5
17452348
Bioinformatics. 2006 Oct 1;22(19):2444-5
16870931
J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31
18952929
Bioinformatics. 2010 Sep 15;26(18):2321-7
20624778
Methods Mol Biol. 2008;453:471-91
18712320
AMIA Annu Symp Proc. 2009 Nov 14;2009:396-400
20351887
In Silico Biol. 2005;5(2):199-208
15972015
Bioinformatics. 2008 Sep 1;24(17):1968-70
18614584
Bioinformatics. 2008 Jun 1;24(11):1410-2
18400773
Inf Retr Boston. 2009;12(1):69-80
19774223
BMC Med Inform Decis Mak. 2005 Dec 01;5:37
16321145
BMC Med Inform Decis Mak. 2007 Jun 15;7:16
17573961
PLoS Comput Biol. 2009 Dec;5(12):e1000597
20041219
AMIA Annu Symp Proc. 2006;:1012
17238631
BMC Bioinformatics. 2008 Feb 19;9:108
18284683
J Biomed Discov Collab. 2008 Feb 15;3:2
18279519
Drug Discov Today. 2005 Mar 15;10(6):439-45
15808823
Biotechniques. 1999 Dec;27(6):1210-4, 1216-7
10631500
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W21-6
17485473
BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S6
20406504
BMC Bioinformatics. 2004 Oct 08;5:147
15473905
Nat Rev Genet. 2006 Feb;7(2):119-29
16418747
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6
15980585
Bioinformatics. 2009 Apr 1;25(7):974-6
18326507
Bioinformatics. 2007 Aug 15;23(16):2196-7
17545178
BMC Med Inform Decis Mak. 2005 Mar 10;5:5
15760470
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W745-7
16845111
Bioinformatics. 2009 Mar 15;25(6):815-21
19188193
PLoS Comput Biol. 2009 Jul;5(7):e1000411
19649304
Bioinformatics. 2007 Jan 15;23(2):e237-44
17237098
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W141-6
19429696
J Biomed Inform. 2011 Apr;44(2):310-8
21094696
Genome Biol. 2008;9 Suppl 2:S4
18834495
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W16-9
15215341
Genome Biol. 2008;9 Suppl 2:S3
18834494
Neural Netw. 2010 Dec;23(10):1208-25
20674268
J Biomed Inform. 2007 Apr;40(2):114-30
16996316
Trends Genet. 1999 Nov;15(11):471-2
10529811
Bioinformatics. 2009 Nov 15;25(22):3031-2
19654114
PLoS Comput Biol. 2008 Jan;4(1):e20
18225946
ACM Trans Knowl Discov Data. 2009 Jul 1;3(3):
20072710
BMC Med Inform Decis Mak. 2007 Jan 10;7:1
17214888
BMC Bioinformatics. 2006 Oct 02;7:424
17014720
Genome Biol. 2008;9 Suppl 2:S8
18834499
Brief Bioinform. 2008 Nov;9(6):452-65
18660511
J Am Med Inform Assoc. 2000 Nov-Dec;7(6):605-17
11062234
Bioinformatics. 2006 Feb 1;22(3):378-80
16332704
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405
18487273
Trends Biochem Sci. 2001 Sep;26(9):573-5
11551795
Mol Cell. 2006 Mar 3;21(5):589-94
16507357