Some new books have become available since the new edition of this book
was published:
Croft, W., Metzler, D., et al. (2009). Search Engines:
Information Retrieval in Practice. Boston, MA. Addison-Wesley.
Hock, R. (2007). The Extreme
Searcher's Internet Handbook, 2nd
Edition: A Guide for the Serious Searcher. Medford, NJ. CyberAge
Books.
Konchady, M. (2008). Building Search
Applications: Lucene,
Lingpipe, and Gate. Oakton, VA. Mustru Publishing.
Chapter 2
2.3 Properties of Scientific Information
New alternatives to the the impact factor: the h-index, g-index, and
others:
Hirsch, J. (2005). An index to quantify an individual's scientific
research output. Proceedings of the
National Academy of Sciences, 102: 16569-16572.
Harzing, A. and vanderWal, R. (2009). A Google Scholar h-index for
journals: An alternative metric to measure journal impact in economics
and business. Journal of the
American Society for Information Science
& Technology, 60: 41-46.
Schreiber, M. (2008). An empirical investigation of the g-index for 26
physicists in comparison with the h-index, the A-index, and the
R-index. Journal of the American
Society for Information Science &
Technology, 59: 1513-1522.
Egghe, L. (2006). Theory and practise of the g-index. Scientometrics,
69: 131-152.
New paper criticizing impact factors:
Campbell, P. (2008). Escape from the impact factor. Ethics in Science
and Environmental Politics, 8: 5-7.
Browman, H. and Stergiou, K. (2008). Factors and indices are one thing,
deciding who is scholarly, why they are scholarly, and the relative
value of their scholarship is something else entirely. Ethics in
Science and Environmental Politics, 8: 1-3.
Lawrence, P. (2008). Lost in publication: how measurement harms
science. Ethics in Science and
Environmental Politics, 8: 9-11.
Simons, K. (2008). The misused impact factor. Science, 322: 165.
2.4 Classification of Health Information
An update of Haynes' 4S model (though I still prefer the 4S!):
Haynes, R. (2006). Of studies, syntheses, synopses, summaries, and
systems: the "5S" evolution of information services for evidence-based
healthcare decisions. Evidence-Based
Medicine, 11: 162-164.
2.5 Production of Health Information
Update on peer review:
Curfman, G., Morrissey, S., et al. (2008). Peer review in the balance.
New England Journal of Medicine,
358: 2276-2277.
Carnevale, R. and Aronsky, D. (2007). The life and death of URLs in
five biomedical informatics journals. International
Journal of Medical
Informatics, 76: 269-273.
Lin, G., Dudley, R., et al. (2008). Frequency of stress testing to
document ischemia prior to elective percutaneous coronary intervention.
Journal of the American Medical
Association, 300: 1765-1773.
Tricoci, P., Allen, J., et al. (2009). Scientific evidence underlying
the ACC/AHA clinical practice guidelines. Journal of the American
Medical Association, 301: 831-841.
Shaneyfelt, T. and Centor, R. (2009). Reassessment of clinical practice
guidelines: go gently into that good night. Journal of the American
Medical Association, 301: 868-869.
2.6 Electronic Publishing
Updates on consumer health searching and other aspects of electornic
publishing:
Tu, H. and Cohen, G. (2008). Striking
Jump in Consumers Seeking Health
Care Information. Washington, DC, Center for Studying Health
System
Change. http://www.hschange.org/CONTENT/1006/.
Dentzer, S. (2009). Communicating medical news - pitfalls of health
care journalism. New England Journal
of Medicine, 360: 1-3.
Yermilov, I., Chow, W., et al. (2008). What is the quality of
surgery-related information on the internet? Lessons learned from a
standardized evaluation of 10 common operations. Journal of the
American College of Surgeons, 207: 580-586.
Starr, S. and Williams, J. (2008). The long tail: a usage analysis of
pre-1993 print biomedical journal literature. Journal of the Medical
Library Association, 96: 20-27.
2.7 Use of Knowledge-Based Health Information
Updates on information-seeking:
Turner, A., Stavri, Z., et al. (2008). From the ground up: information
needs of nurses in a rural public health department in Oregon. Journal
of the Medical Library Association, 96: 335-342.
Abrahamson, J., Fisher, K., et al. (2008). Lay information mediary
behavior uncovered: exploring how nonprofessionals seek health
information for themselves and others online. Journal of the Medical
Library Association, 96: 310-323.
Hemminger, B., Lu, D., et al. (2007). Information seeking behavior of
academic scientists. Journal of the
American Society for Information
Science & Technology, 58: 2205-2225.
Chapter 3
3.2 Bibliographic Content
Microsoft has abandoned Windows Academic Live, its competitor to Google
Scholar.
3.3 Full-text Content
Papers from the AMIA Annual
Symposium Proceedings (and the Symposium
for Computer
Applciations in Medical Care, or SCAMC, before it) are all
available
now in PubMed Central: http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=362&action=archive
Other informatics-related journal content available in full-text in
PubMed Central include:
Medpedia (http://www.medpedia.com/)
is a no-cost online medical encyclopedia that employs trained medical
professionals will be permitted to write and edit the site. Each author
will have a contributor page that details his or her experience and
qualifications.
Another model organism database is the Zebra Fish Information Network (http://zfish.uoregon.edu/). I had
a chance to visit the Zebra Fish colony in Eugene!
Chapter 4
4.3 Controlled Vocabularies
A questionnaire about the use of the UMLS by informatics researchers
had responses from 70 users. The two major intended uses were access to
source terminologies (75%) and mapping among source terminologies
(44%). The most common reported uses were:
Terminology research (31%)
Information retrieval (16%)
Terminology translation (12%)
Others reported UMLS was used as a terminology itself (77%) and stated
they wanted NLM to develop unified hierarchy and derive a terminology
(73%).
Chen, Y., Perl, Y., et al. (2007). Analysis of a study of the users,
uses, and future agenda of the UMLS. Journal
of the American Medical Informatics Association, 14: 221-231.
A primer on the OAI-ORE project has been published: Lagoze C and van de
Sompel H, ORE User Guide - Primer. 2008, Open Archives Initiative, http://www.openarchives.org/ore/1.0/primer.
6.4 Copyright and Intellectual Property
Biomed Central (BMC) has been sold to publishing conglomerate Springer
(publisher of my book). No changes are planned in the operation of BMC
for now. Time will tell.
Gawrylewski, A. (2008). BioMed Central sold to Springer. TheScientist.com. October 7, 2008. http://www.the-scientist.com/blog/display/55074/.
More details on the NIH Public Access Policy. The NIH Public Access
Policy aims to ensure that the public has access to the published
results of NIH-funded research. It requires scientists to submit their
final peer-reviewed journal manuscripts that result from NIH funding to
PubMed Central upon acceptance for publication no later than 12 months
after publication.
Address Copyright - Ensure that the journal's publishing
agreement allows the paper to be posted to PubMed Central in accordance
with the the NIH Public Access Policy
Submit Papers - Submit final submitted manuscript or published
paper to PubMed Central
Cite Papers - Include the PMCID at the end of the full citation
of the article whenever it is cited
The policy applies to any manuscript that:
Is peer-reviewed
Is accepted for publication in a journal on or after April 7, 2008
Arises from:
Any direct funding from an NIH grant or cooperative agreement
active in Fiscal Year 2008 or beyond
Any direct funding from an NIH contract signed on or after
April 7, 2008
Any direct funding from the NIH Intramural Program
An NIH employee
6.5 Preservation
A new report commissioned by the National Science Foundation (NSF,
2008) highlights some of the issues and challenges for digital
preservation. It concludes the following:
Inadequacy of funding models to address long-term access and
preservation needs
Confusion and/or lack of alignment between stakeholders, roles,
and responsibilities with respect to digital access and preservation
Inadequate institutional, enterprise, and/or community incentives
to support the collaboration needed to reinforce sustainable economic
models
Complacency that current practices are “good enough”
Fear that digital access and preservation is too big to take on
Anonymous (2008). Sustaining the Digital Investment: Issues and
Challenges of Economically Sustainable Digital Preservation, Blue
Ribbon Task Force on Sustainable Digital Preservation and Access.
http://brtf.sdsc.edu/biblio/BRTF_Interim_Report.pdf.
6.6 Librarians, Informationists, and Other Professionals
An “ask the doctor” text-based consultation service in Sweden was
recently described, reporting 38,217 inquiries over 4 years (Umefjord,
2008).
Umefjord, G., Sandström, H., et al. (2008). Medical text-based
consultations on the Internet: a 4-year study. International Journal of Medical
Informatics, 77: 114-121.
Chapter 7
7.4 Searching Quality
Leroy et al. (2007) compared three systems:
Medtextus – keyword suggestion, results organized by folders
Helpful Med – keyword suggestions, topic maps
NLM Gateway – access to wide variety of resources
They assessed 23 users searching on 12 topics. The outcome measures
were effectiveness (subtopics retrieved) and efficiency (searches
required). They found no difference in effectiveness but Medtextus was
more efficient and Helpful Med had higher user satisfaction.
Leroy, G., Xu, J., et al. (2007). An end user evaluation of query
formulation and results review tools in three medical meta-search
engines. International Journal of
Medical Informatics, 76: 780-789.
Chapter 8
8.1.2 Linguistic Systems
The NLM has made available a suite of Java programs called the
SPECIALIST NLP tools that provide a variety of programs for aspects of
medical NLP at http://lexsrv3.nlm.nih.gov/SPECIALIST/.
8.1.3.4 Medical image retrieval
The ImageCLEFmed task goes on. A paper has been published by Hersh et
al. (2009) describing the consolidation of the test collections from
2005-2007. In addition, for the 2008 task, a new image collection was
developed from the Goldminer collection, which contains images in
figures from several radiology journals published by Highwire Press.
Hersh, W., Müller, H., et al. (2009). The ImageCLEFmed medical
image retrieval task test collection. Journal
of Digital Imaging. Epub ahead of print.
Müller, H., Kalpathy-Cramer, J., et al. (2008). Overview of the
ImageCLEFmed 2008 medical image retrieval task. Working Notes for the CLEF 2008 Workshop,
Aarhus, Denmark. http://www.clef-campaign.org/2008/working_notes/ImageCLEFmed2008_Overview.pdf.
* denotes this material has not yet been incorporated into my OHSU
course, BMI 514 - Information Retrieval.
