Guide to Library Research in Cell Physiology

An important factor in your academic and professional success will be how well you develop the ability to determine when you need information and to locate, evaluate, and use it effectively. One of the goals of the research assignments in this course is to help you to strengthen these “information literacy” skills. In order to complete the assignments in this course, including the grant proposal, you will be required to locate background information, physical property data, experimental protocols or techniques, and articles from the primary scientific literature. In addition, cell and molecular biology research requires knowledge of bioinformatics techniques for accessing and analyzing nucleotide and protein sequence data.

This guide supplements the Cell Physiology course web page prepared by Dr. Fraga. It parallels and links to lessons from the Guide to Library Research in Science, with additional emphasis on the special tools and resources needed for Cell Physiology and other courses in the Biochemistry and Molecular Biology major. Combined with in-class instruction, these integrated web guides will:

• discuss the importance, evolution and organization of scientific information;
• provide suggestions for developing search strategies;
• suggest specific reference sources and general browsing strategies to use as a starting point;
• explain the organization of The College of Wooster libraries;
• introduce techniques for using library catalogs, research databases, and the World Wide Web;
• provide advice on how to evaluate the quality of the information you gather; and
• discuss the ethical use of information, including citing sources.

Remember — The primary goal of the Timken Science Library staff is to help you to develop the skills needed to locate, evaluate, and use information effectively. If you have questions, ask for assistance at one of the staffed service points or the librarian’s office, or contact us by telephone or e-mail. To request an individual appointment for research assistance on a specific topic or assignment, complete and send the Science Library Reference Consultation Request Form. The Science Librarian will contact you to set up an appointment.

The Structure of Scientific Communication

Science is sustained by its literature, which is both the foundation for and a product of continuing progress in scientific research. Knowledge of the research and publication cycle in the sciences will greatly enhance your efficiency in approaching the literature. See Lesson 2: Scientific Communication of the Guide to Library Research in Science for more information about this topic. The Evolution of Scientific Information provides a graphical representation of the process beginning with the production and dissemination of newly generated experimental or theoretical information through various primary sources, including journal articles, patents, theses and dissertations, and conference papers. In addition to bibliographic sources, nucleotide and amino acid sequences deposited in archival sequence databases such as GenBank and SWISS-Prot are also primary information sources.

Secondary sources facilitate access to the assimilation of information found in widely dispersed primary literature and data sources. These secondary sources are the familiar reference tools such as handbooks, encyclopedias, and dictionaries, used to locate specific data, background information, and definitions of terms. See Lesson 3: Reference Sources for descriptions of the different kinds of reference sources. Lists of reference tools available for each discipline can be found on the Subject Guides page. The guide for Biochemistry and Molecular Biology will be the most useful for this course, but you may also want to look at the guides for Chemistry, Biology, and Medicine and Health. To retrieve a more extensive list  of relevant sources, complete the Selected Bibliography of Science Reference Sources form.

Search Strategies and Tools

One strategy for locating materials in the library, particularly reference materials, is to browse the collection by subject area. Knowledge of library classification systems facilitates browsing and locating materials retrieved by searching the library catalog. Lesson 4: Organization of Library Materials of the Guide to Library Research in Science discusses library classification systems used at the College of Wooster libraries, as well as physical locations within the libraries.

Lesson 5: Search Strategies and Techniques guides you through the steps for developing a good strategy starting with defining your search question, identifying the major concepts of the topic and listing keywords that describe each concept. The lesson also provides an introduction to the general search techniques, including Boolean and proximity operators, truncation and subject vs keyword searching. These techniques apply in most databases.

Library catalogs contain listings of the materials owned by (or accessible from) their respective libraries. Lesson 6: Searching Library Catalogs provides a description of the contents of the CONSORT and OhioLINK library catalogs, as well as important features of these databases that will help you retrieve relevant materials on your search topic.

Finding Primary Scientific Sources

Primary sources in science present information that has not been previously published in any form in any other source. The information presented is a direct result of scientific research and may be communicated through either formal or informal channels. Journal articles, patents, and technical reports are examples of primary literature that have been evaluated through a peer-review process and are disseminated through published sources. Researchers locate references to these primary sources using bibliographies and electronic bibliographic databases.

Lesson 7: Finding Citations to Articles in Periodicals provides access to extensive information on finding periodical articles and other primary sources, including descriptions of science databases and search systems, and tutorials and help screens describing the structure and search techniques for the many science databases available at The College.

Searching PubMed

PubMed is the primary bibliographic database you will use in your research assignments in Cell Physiology. PubMed, a service of the National Library of Medicine, includes citations for biomedical articles dating back to the 1950s. Entrez is the integrated search and retrieval system used for PubMed and the biosequence databases created and maintained by the National Center for Biotechnology Information (NCBI) to provide access to nucleotide and protein sequence data, 3D protein structures, and genomic mapping information, as well as to bibliographic citations to the primary biomedical literature and full text of many articles.

The National Library of Medicine (NLM) has produced excellent tutorials and other documentation to help you understand the database and how to search it. The most complete and detailed is the web-based PubMed Tutorial, which contains animated demonstrations of procedures. This tutorial requires a significant investment in time, but covers all of the features and search procedures thoroughly and is well worth the time.

In addition to this comprehensive tutorial, NLM has produced a series of animated Quick Tours, each of which focuses on a single search technique in PubMed. These include searching by author, by author and subject, by simple subject, searching for a journal and retrieving citations from a single journal issue. Each of these tutorials is about one to three minutes in length.

Once you have learned the simple search techniques illustrated in these tutorials, you will want to learn how to use the MeSH database of controlled vocabulary terms. NLM provides three Quick Tours illustrating how to search the MeSH database, to combine MeSH terms, to apply subheadings and other features of the MeSH database. These tutorials run approximately three to five minutes.

Locating the Full Text of Journal Articles and Other Documents

Lesson 8: Understanding Citations provides assistance in interpreting bibliographic citations retrieved from print indexes, electronic bibliographic databases, or bibliographies found in books, articles, or other sources. To determine how to access a journal article cited in a print index, an electronic database, a bibliography or other source, follow the procedure outlined in Lesson 9: Finding Full Text of Journal Articles. One of the advantages of membership in the CONSORT and OhioLINK consortia is that College of Wooster students have access to the resources of many academic libraries, in the state of Ohio. And, if the required materials cannot be found in Ohio, they can usually be obtained from outside the state. Lesson 11: Borrowing from Other Libraries describes procedures for accessing resources held off campus.

Bioinformatics

The rapidly evolving field of bioinformatics, which integrates molecular biology and computational methods, provides scientists with new tools with which to access, evaluate, and integrate the large quantities of nucleotide, amino acid and gene sequence data being generated experimentally into their own research. These data become another type of search term to be used in searching bibliographic and other integrated databases. It is essential for students working in the related fields of molecular biology, biochemistry and genetics to learn to access and manipulate the information contained in the hundreds of databases that serve as repositories for the experimentally generated data. These databases may be comprehensive, containing many kinds of sequences from many different organisms, or they may be specialized, containing information from specific organisms, from specific categories of sequences, or from specific sequence technologies.

The ExPASy Life Science Directory provides an extensive list of databases and reference sources related to bioinformatics. Choosing appropriate databases from such a list can be an overwhelming task for a beginner. A better strategy is to use a single search system that combines information from related databases.

The Entrez search and retrieval system provides a seamless interface for searching the integrated suite of databases developed by the National Center for Biotechnology Information (NCBI) and their international partners. Using the Entrez system, you can retrieve protein and nucleotide sequence data, 3D protein structures, genomic mapping information and references to the biomedical literature by entering author names, gene or protein names, subject keywords, organisms, journal titles, and many other terms or identification numbers. Entrez provides links from a record in one database to related records in other databases. See the Model of Entrez Databases for an illustration of the connections between Entrez databases.

Searching for Nucleotide and Protein Sequences

The Entrez Nucleotides and Entrez Protein databases contain sequences from several sources, including GenBank, SwissProt, GenPept, PDB, RefSeq, and other sources. Records in these databases may be archival, containing raw sequence data as submitted by researchers, or they may be curated, containing value-added information. For descriptions of the data contained in the different kinds of records in these databases, see Reading Sequence Records.

Searching the World Wide Web

The World Wide Web is an increasingly valuable source for all kinds of information. The Web has made enormous quantities of information accessible that previously would have been unavailable. At the same time the Web makes it possible for almost anyone to share ideas, information and opinions with others around the world. It is important to learn to search this vast network efficiently and to evaluate everything you retrieve. See Lesson 10:Searching the World Wide Web for more information on Web search tools and search strategy. There is also an excellent interactive tutorial produced by The Ohio State University Libraries at net.Tutor. See Selected Internet Sites on the Biochemistry and Molecular Biology subject guide page for links to helpful gateways, databases, analysis tools, reference sources and tutorials, and research laboratories and organizations.

Evaluating Information

Critical evaluation of information is an essential part of the research process. Whether the source of your information is a print reference or a web site, it is important to evaluate the information for accuracy, authority, timeliness, coverage and objectivity. See Lesson 12: Evaluating Information for tips on assessing the reliability of information from both print and World Wide Web resources. The University of California at Berkeley tutorial titled Finding Information on the Internet: A Tutorial includes a page, Evaluating Web Pages: Techniques to Apply and Questions to Ask, that provides helpful strategies for evaluating web sites and a handy Web Page Evaluation Checklist.

Ethical Use of Information and Citing Sources

Michael Faraday listed three necessary stages of useful research: to begin it, to end it, and to publish it.* The importance of communication in the sciences arises from the fact that the objective knowledge of science is cumulative in nature. Each new bit of knowledge adds to, modifies, refines, or sometimes refutes that which came before. Scientists hope that their work will prove useful to others in the advancement of science. Using another’s work without proper attribution amounts to theft of intellectual property, or plagiarism. Lesson 13: Ethical Use of Information discusses the concepts of academic integrity and plagiarism and links to a site that provides advice on how to recognize and avoid plagiarism.

In addition to crediting other researchers for their work, citing references in research papers and publications guides others to the original article. It is essential that all of the information needed to locate the original document is present in the citation and is accurate. Incorrect citations cost time and are frustrating for researchers.

*Allan Kent and Harold Lancour, eds. Encyclopedia of Library and Information Science (New York: Dekker, 1979), s.v. “Scientific Literature,” by K. Subramanyam, 391.

Formating Citations

Different academic disciplines and publications use different styles for citing sources. Lesson 13: Ethical Use of Information lists a few of the many style guides that may be helpful. The style that Dr. Fraga prefers for your work in the cell physiology course is the style used in the journal Cell. The following are examples of citations to articles and books.

Citing an Article in a Periodical

Sondheimer, N., and Lindquist, S. (2000). Rnq1: an epigenetic modifier of protein function in yeast. Molecules and Cells 5, 163-172.

Note —

• Author names should be in reverse order, with first and middle (when available) initials.
• "et al." should only be used after 10 authors.
• Publication date should be enclosed in parentheses and followed by a period.
• Article title should be in lower case except for the first word and proper nouns.
• Although the citation format in Cell uses journal title abbreviations, Dr. Fraga wants you to provide the FULL journal title with important words in upper case. See the PubMed Journals Database to locate the full journal title.
• The journal title appears in plain text — not italics, not bold.
• There is no punctuation between the journal title and the volume number.
• The volume number is italicized and followed by a comma, space and page numbers.

Citing an Article in a Book

Sorenson, P.W., and Caprio, J.C. (1998). Chemoreception. In The Physiology of Fishes, D.H. Evans, ed. (Boca Raton, FL: CRC Press), pp. 375-405.

Citing an Entire Book

Cowan, W.M., Jessell, T.M., and Zipursky, S.L. (1997). Molecular and Cellular Approaches to Neural Development (New York: Oxford University Press).

The same principles apply in citing web sources as in print. The important considerations are providing attribution to the authors/creators, and providing accurate information that allows access to the site. Some elements of a Web citation may be missing, but you should cite what is available. An additional element required in citing Web sources is the date you accessed the site. This information is important because Web sites change and move so frequently.

The following examples of citations to Internet sources are consistent with the Cell citation format.

Citing a Web Site

Fraga, D. (March 5, 2004). Ciliates in the Classroom. Retrieved January 6, 2005, from The College of Wooster, Biology Department Web site: http://www.wooster.edu/biology/Ciliates/Ciliates_in_the_Classroom.html

Citing Part of a Larger Web Site

Fraga, D. (July 2, 2001). Background information about ciliates. In Ciliates in the Classroom. Retrieved January 6, 2005, from The College of Wooster, Biology Department Web site: http://www.wooster.edu/biology/Ciliates/citc/Background.html

Citing a Magazine, Journal or Newspaper Article Retrieved from a Subscription Database

Houston, R.D., Cameron, N.D., and Rance, K.A. (2004). A melanocortin-4 receptor (MC4R) polymorphism is associated with performance traits in divergently selected large white pig populations. Animal Genetics 35, 386-390. Retrieved on January 6, 2006, from EBSCOhost.

The Citing Net Sources lesson of The Ohio State University Libraries’ net.Tutor provides very helpful information and examples for citing electronic sources.

Don’t Forget — The information presented in your in-class library instruction session and on this web site are intended as an introduction to library research. As you begin to gather and evaluate information for your research  paper, you will probably have questions about research methods  or resources that have not been covered in class or on this web site. If you have any questions, ask the Science Librarian for help.