Biobliographic Searching

Bibliographic Searching for Fun and Profit
in the Bioinformatic Sciences

Lynda Ellis, October 24, 2002

[MICa 8006 Home Page]

Introduction

There is a wealth of information available to you if you make effective use of bibliographic search engines. Some are available to everyone with Web access; others require that you have University of Minnesota X.500 authentication. This authentication is the user name you are given when you register for a course or are employed by the University (the official umn.edu user name, not another account on a different server), plus the password you chose when you activate this UM official e-mail account. You don't need to use this account for e-mail (you can set it to forward e-mail to another account); you do need to activate it and remember the username and password.

Good lists of all bibliographic resources are available from the University of Minnesota Library's General Index page http://www1.lib.umn.edu/articles/indexes.phtml

Including Indexes in Agriculture, Biology and Ecology http://www.lib.umn.edu/articles/agri.phtml

Indexes in Health Sciences http://www.lib.umn.edu/articles/subject.phtml?SubjectID=401

and Indexes in Computer Science http://www1.lib.umn.edu/articles/subject.phtml?SubjectID=166

Also, for access to online versions of papers, there is a list of EJournals (journals that UMn library users have electronic access to) http://www.lib.umn.edu/articles/ej.phtml

Entrez PubMed

One freely available resource of great use in molecular biology and biomedicine is National Center for Biotechnology Information (NCBI) Entrez PubMed,
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=umnbmlib.

If you access PubMed using the above URL, it will indicate articles that UMn subscriptions allow you electronic access to full-text. You can search all of Medline (and more) back to 1966 in complex ways. PubMed provides help.

The journals selected for Medline cover the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. That is, all bioinformatic journals are NOT covered.

Current Contents and Science Citation Index

More journals are covered, but not as far back, in two other bibliographic databases restricted to University of Minnesota X.500 (or other) authenticated access. These are Current Contents, accessed through the OVID system,
https://www.biomedsearch.lib.umn.edu/ovidweb/ovidweb.cgi,
and Science Citation Index Online, also called "Web of Science."
http://www.lib.umn.edu/web-bin/isi.cgi.

Current Content Searching

After you sign on to the OVID system, you select the databases you wish to search. Chose Current Contents/All Editions.

By default, Current Contents allows you to search on words or phrases in the abstract, title, author keywords, and keywords plus, and optionally limit your search to Ovid Full-text, English language, Articles, Reviews, and/or Abstracts, and some other fields. You can further restrict your searches if desired.

Example Current Contents Searches

A Current Contents Author Search on "Essenberg M" retrieved 12 citations by this author on October 24, 2002. The titles of the hits are displayed 10 per page. Relevant citations are selected by clicking on the check box in front of the citation number; the Citation Manager at the bottom on of each display page can be used to display the complete abstract for all or the selected citations.

A Current Content default Search on "bioinformatics" done on October 24, 2002 returned 1045 citations. When limited to title written in English, 1030 remained, still too many to review. Choosing "Title" at the top of the search page, then limiting the last search to the article title, returned 323 citations. Again, hits could be reviewed 10 at a time; relevant citations could be selected by clicking on the check box in front of the citation number; the Citation Manager at the bottom on of each display page can be used to display the complete abstract for all retrieved or only the selected citations.

Science Citation (Web of Science) Searching

Science Citation Online offers some different ways to search the scientific literature. It only contains 1997 to present literature. But you can use a Full Search to conduct searches on a topic or by author and also to find articles which cite these works or which use related references. That is, if you know a relevant reference (possibly found in PubMed or Current Contents), you can find the most recent papers which cite this reference. Or if you find a relevant paper in Science Citation Online, you can find other recent papers which cite the same references as does that paper. Optionally, you can select those cited references which are especially relevant, and limit the "related references" to those which cite only these.

From the Institute for Scientific Information (ISI) home page, select a Full Search. On the Full Search page, choose: Science Citation Index Expanded (SCI-EXPANDED)--1997-present, by checking the box in front of its name (NOT clicking on the name). Next choose either a General Search (similar to searching the other bibliographic databases) or a Cited Reference Search (where you search for works which cite a given reference).

Example Science Citation Searches

A General Search on the author "Klopman G" retrieved 41 articles on March 2, 2000. The eigth one (Klopman, Tu and Fan) was especially relevant and was not available in Entrez Medline. The full abstract was retrieved by clicking on its title. At the top of the full abstract page was the "related records" button. Clicking that produced 254 hits, some of which were relevant.

The full abstract of the Klopman, Tu and Fan article had a link toward the top of the page which said "Cited References: 27". This means it had 27 citations; clicking on that showed all of them. Selecting the most relevant 6 of these and then clicking "related records" produced a more relevant list of 20 hits.

A Full, Cited Reference Search for name: KLOPMAN G, cited work (which means journal name): ENVIRON TOXICOL CHEM, and year: 1995, found one cited reference with those characteristics. Selecting it (checking the box in front of it) and choosing "Search" found 9 relevant references which cited it.

INSPEC

INSPEC, another bibliographic database limited to those with UM X.500 access, covers, among other topics, computing and information technology.
http://www.lib.umn.edu/web-bin/ovid-inspec.cgi

INSPEC is available through OVID, on a different OVID server than the one used for Current Contents. You can chose INSPEC 1997-latest, INSPEC 1969-latest, or INSPEC 1969-1996. To chose a database, click on its name.

A search for "protein sequence analysis" in INSPEC 1997-Aug 2002, returned 7 hits on October 25, 2002, both journal and conference papers, only one of which was also indexed in PubMed.

SCIFINDER

SCIFINDER is a bibiographic and other database search engine, specifically for chemistry and related fields. It requires download of special software.
http://sciweb.lib.umn.edu/subject/software/scifinder.phtml

IEEE Explorer

IEEE Explorer is a another special purchase tool to search the engineering and computer science publications of IEEE.
http://ieeexplore.ieee.org/Xplore/DynWel.jsp

Search Strategy

The best search strategy depends on what you are looking for and where you are looking for it. If you have important information needs, don't depend on any ONE journal, bibliographic search engine, or type of search. Each bibliographic search engine listed above has limitations; there are others which may be better for any given search.

Keep track of your searches. Some of the engines allow you to store them so they can be rerun or revised. Entrez permits you to write search URLs which can be rerun as you desire.

And be open to serendipity. When searching the library stacks for books, you may come across an unexpected treasure. Paging through a paper journal may provide the same pleasant surprises. This can also happen with an electronic search; you may explore some "irrelevant" articles and perhaps discover relevance where you did not expect it.