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Bioinformatics Training by Librarians and for Librarians: Developing the Skills Needed to Support Molecular Biology and Clinical Genetics Information Instruction

Kristine Alpi
Lecturer in Public Health, Weill Medical College of Cornell University
Library Manager, New York City Department of Health & Mental Hygiene
kalpi@att.net

Abstract

Bioinformatics draws on a variety of sources -- computational biology, computer science, molecular biology, genetics, information technology (IT) -- and has been defined many ways. According to Luscombe et al. (2001), bioinformatics is "conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying 'informatics' techniques (derived from disciplines such as applied maths [sic], computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale." While librarians may find themselves overwhelmed by definitions like these and the content of bioinformatics resources, the focus on organization of information and database structures should be familiar ground.

As with any other multidisciplinary subject, there are many avenues for building knowledge and skills in bioinformatics: hands-on and lecture classes in the curriculum, workshops on specific techniques or software, self-directed learning by online tutorials or reading one of the journals now devoted to this topic. This article outlines some of the opportunities for expanding bioinformatics knowledge and leveraging this knowledge into a teaching role.

Introduction

As the field of bioinformatics expands, there is an ongoing effort to understand the information and training needs of bioinformatics practitioners. This research has been done in other areas of informatics, but those disciplines will not be addressed in this article. The audience for bioinformatics training is bifurcated: training computer science and information technologists to understand the nuances of systems for computational biology; and training biologists and other scientists to have a better idea of how information technology (IT) can be applied to their problems. Dubay et al. propose a taxonomy illustrating the range of applications, technologies and skills employed in bioinformatics. The taxonomy was used for a needs assessment that was then used to inform a curriculum attempting to deliver the identified skills to a broad audience (Dubay 2002). Stevens et al. reported on a survey of bioinformatics tasks undertaken by working biologists to find the range of tasks that need to be supported through training (Stevens et al. 2001).

The idea that the librarian has a role in searching and teaching bioinformatics resources is not new. The National Center for Biotechnology Information (NCBI), the producer of GenBank and many other bioinformatics resources, is part of the National Library of Medicine. NCBI staff published an article about their resources in the Bulletin of the Medical Library association in 1993 (Woodsmall et al). In articles from 1997 and 1999, Norman recommended that medical librarians should have a basic understanding of the type of information contained in key genetic information resources and know how to search them. Generally, librarians with a science background or a liaison relation with science or IT departments find it easier to develop these roles.

Background

The terminology of bioinformatics is enough to frighten away the uninitiated. The literature discussing information resources and training in this area often uses some of the following terms interchangeably.

Bioinformatics

science of managing and analyzing biological data using advanced computing techniques

Computational Biology

field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions.

Genetics

study of inheritance patterns of specific traits

Genomics

study of genes and their function

Molecular Biology

discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.

The NCBI web site addressed the issues of complex terminology and lack of scientific background by creating a {Science Primer} which explains and illustrates the primary processes of genomics and bioinformatics.

There are many ways to support education and outreach in bioinformatics. In a library-based bioinformatics needs assessment, Yarfitz and Ketchell outline three levels of knowledge for meeting information needs:

1. Basic Questions: Locating resources, programs or databases
2. Technical Questions: Identifying appropriate tool for research or clinical needs
3. Analytical Questions: Planning experiments or in-depth assistance with data analysis

They indicate that all librarians can meet the basic questions category with a little training. Handling the technical questions level requires some ongoing current awareness and hands-on experience with some of the software and databases. The analytical questions generally require significant background in biology (Yarfitz & Ketchell 2000). There are many formal and informal opportunities for librarians to gain training to help them address basic and technical questions. Several of these strategies have been promoted via conference posters (Alpi et al. 2001) and presentations.

Training Opportunities

Training can be employer-directed, group-directed, or self-directed. Self-directed learning is common in bioinformatics with many online tutorials for software and techniques, as well as journals such as Bioinformatics. The six-month electronic journal club on bioinformatics in 2001-02 in which librarians from the Medical Informatics section and the Molecular Biology & Genomics SIG of the Medical Library Association participated represents group-directed learning. Lyon describes a bioinformatics training program for health sciences librarians at Vanderbilt University that involves subject knowledge, literature evaluation, and database searching techniques (Lyon 2003).

The NCBI offered a one-day course for librarians new to bioinformatics for several years. This course has been transitioned into a three-day course for librarians and information professionals entitled Introduction to Molecular Biology Information Resources. This course provides an introduction to four domains of information generated by the field of molecular biology:

• nucleotide sequences
• protein sequences
• three-dimensional structures
• complete genomes and maps

An overview of search systems, including Entrez and LocusLink, emphasizes how librarians' current search skills apply to molecular biology databases. The course also introduces more technical search systems, including BLAST and Map Viewer, as well as the Cn3D viewer for three-dimensional protein structures. The course format combines lecture, demonstration, and hands-on experience, and concludes with a discussion of various levels of molecular biology information services provided by librarians.

NCBI also offers a five-day Advanced Workshop for Bioinformatics Information Specialists. It is designed for full-time bioinformatics specialists based in libraries, including scientists who have been hired for these specialized positions as well as bioinformatics librarians. A science background or knowledge of molecular biology and genetics, and experience with the resources covered in this introductory course is required. Additional courses can be located through the Medical Library Association's {Continuing Education Clearinghouse} selecting the general subject "Molecular Biology."

Self-education tutorials abound on the web. There are tutorials on BLAST, the human genome, structure viewing and nucleotide searching on the NCBI Education page. Vanderbilt University offers librarian-designed tutorials on genetic databases.

If classroom training is sought, there are full-time curricula available. The American Society of Information Science and Technology 2002 conference offered a special session on "Bioinformatics in Information Science Education." The author shares his PowerPoint presentation on how bioinformatics is being included in curricula in the United States. Also linked to this document is the listing of bioinformatics programs in fall 2002, with detailed information on content, host department, entrance and completion requirements, and links to program web pages.

Unfortunately, the level of bioinformatics exposure in most library and information science graduate programs is limited. Here are two examples from the author's experience. At the Palmer School of Library & Information Science, the science librarianship course in 2001 offered one two-hour session on molecular biology resources which included an assignment on profiling a database from the Nucleic Acids Research database issue. Although several of the students had a science background or experience in science libraries, they reported the class content to be somewhat overwhelming. A session on NCBI resources was also offered during the spring 2003 health sciences librarianship course at Rutgers University. Repeated exposure to bioinformatics concepts and resources will be necessary to ensure creating a cadre of librarians willing to further their skills in this discipline.

Keeping Up with Bioinformatics

Users of molecular biology information resources often use the resources they know, get some of the information they need, and move on. As the number and complexity of available resources grows, users might not be aware of better approaches or tools. Librarians can have significant impact by employing current awareness strategies to keep up with the plethora of available resources. One of the main resources is the annual database issue of the journal Nucleic Acids Research that appears in January. It includes a {categorized list of databases}. There are many electronic discussion lists and web sites to explore.

• {Molecular Biology & Genomics SIG} - Medical Library Association
• {Sigbioinform-l Mailing List} - American Society for Information Science and Technology
• {Genomics Working Group} - American Medical Informatics Association

Discussion

While some science faculty members welcome librarian participation in their courses, there may be others who think librarians are not capable of teaching non-bibliographic databases. Parlaying previous experience teaching other statistical or databank resources may be one way to change this perception. By offering and advertising library-based courses in bioinformatics databases, librarians can promote their ability to provide support and training on these resources. Many institutions provide bioinformatics support services through the Information Systems department or a specialized support person. The librarians involved with the NCBI NAWBIS course identified various approaches to communicate the types of tools and services available. Through their initial successes in demonstrating key points in searching bioinformatics resources, information specialists' contributions to education, research, and clinical practice became an integral and important part of the genetic and molecular biology programs (Alpi 2002).

Science librarians are often involved in the teaching of searching skills to first-year students in college and graduate and medical schools. There have been several examples of health science and science librarians' existing and planned involvement with teaching bioinformatics searching skills in the curriculum. Some instructors approach the material as an outline of the databases, while others build clinical or scientific cases that allow a more problem-based exploration of the resources.

Delwiche described a group of databases, including NCBI's GenBank, LocusLink, RefSeq, OMIM, and Genes and Disease, and outlined a proposed instructional program teaching these databases in an undergraduate genetics course at the University of Vermont (Delwiche 2001). Tennant (2002) outlined her experience teaching in a genetics class. At Washington University School of Medicine (WUSM), a first-year student module not involving librarians uses clinical cases to explore information in GenBank, Online Mendelian Inheritance in Man (OMIM), and PubMed databases (Magee et al. 2001).

Conclusion

Bioinformatics has become established as a discipline with its own vocabularies, professional journals, and training programs. There is currently a lack of librarians well versed in the discipline to fully explore opportunities in collaborative teaching in this area. Science librarians can use of a variety of resources and methods to prepare themselves for a partnership role in teaching bioinformatics databases to students and faculty on a variety of levels.

Note: The author has received funding from the National Library of Medicine to participate as an educational collaborator for the National Center for Biotechnology Information bioinformatics workshops.

References

Alpi, K. 2002. Outreach and Communication Module. NCBI Advanced Workshop for Bioinformatics Information Specialists. [Online] Available: {http://web.archive.org/web/20070221181534/http://library.med.cornell.edu/Library/nahsl/molbioposter.pdf} [January 10, 2003].

Alpi, K. M., Hendler, G. Y. & Ohles, J. 2001. Making Sense of Molecular Medicine: New York Librarians' Involvement with Bioinformatics. NAHSL/NY-NJ Information & Technology, Oct. 15, 2001. [Online] Available: http://library.med.cornell.edu/Library/nahsl/molbioposter.pdf} [January 10, 2003]

Delwiche, F. A. 2001. Introduction to resources in molecular genetics. Medical Reference Services Quarterly 20(2):33-50.

Dubay, C. J., Brundege, J.M., Hersh, W. & Spackman, K. 2002. Delivering bioinformatics training: bridging the gaps between computer science and biomedicine. Proceedings of the AMIA Annual Symposium: 220-4.

Luscombe, N. M., Greenbaum, D, & Gerstein, M. 2001. What is bioinformatics? A proposed definition and overview of the field. Methods of Information in Medicine 40(4):346-58.

Lyon, J. Beyond the Literature: Bioinformatics Training for Medical Librarians. Medical Reference Services Quarterly 22(1):67-74.

Magee, J., Gordon, J. I. & Whelan, A. 2001. Bringing the human genome and the revolution in bioinformatics to the medical school classroom: a case report from Washington University School of Medicine. Academic Medicine 76(8):852-5.

Norman, F. 1997. Bioinformatics to bioinformation -- a role for librarians. CCP11 Newsletter 1.2(2). [Online]. Available: {http://www.dl.ac.uk/CCP/CCP11/newsletter/vol1_2/bioinformation.html} [January 10, 2003].

________. 1999. Genetic information resources: a new field for medical librarians. Health Libraries Review 16(1):15-28.

Stevens, R, Goble, C, Baker, P & Brass, A. 2001. A classification of tasks in bioinformatics. Bioinformatics 17(2):180-8.

Tennant, M. R. & Miyamoto, M. M. 2002. The role of the medical library in undergraduate education: a case study in genetics. Journal of the Medical Library Association 90(2):181-93.

Woodsmall, R.M. & Benson, D. A. 1993. Information resources at the National Center for Biotechnology Information. Bulletin of the Medical Library Association 81(3):282-4.

Yarfitz, S. & Ketchell, D. S. 2000. A library-based bioinformatics services program. Bulletin of the Medical Library Association 88(1): 36-48.

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