Bioinformatics

A Venn diagram depicting overlap in informatics

To browse other articles on a range of HSL topics, see the wiki index.

Introduction

see also Medical informatics, Knowledge translation and synthesis & Nucleotide searching

"...bioinformatics can be defined as the use of computers and computer science to study biological questions; it forms the intersection between molecular biology, related biological disciplines and computer science. This interdisciplinary field involves researchers who work at many different points on the computer science-biology spectrum. From those who develop new algorithms to those who use computational applications to study biological phenomena, and gain new insight into the life sciences, identify new drug targets etc. The field is currently evolving, but one point is agreed upon: bioinformatics is a field within which there remain many significant discoveries to be made.
~ Bioinformatics at SFU definition

Bioinformatics is the integration of computers, databases and software into research projects that address large biological questions, or problems. Approaches to bioinformatics are often used to generate large sets of information or data. Two large-scale clinical bioinformatics domains are applied genomics, and proteomics, the study of proteins. While bioinformatics describes the use of computers to manage biological information -- it is both an information science as well as a biological one. In a sense, the definition used most often is even narrower: bioinformatics is a synonym for computational molecular biology or the use of computers to understand living things at a molecular level. (For an introduction to this topic, see this Bioinformatics primer).

Genomics is the branch of molecular biology concerned with the structure, function, evolution and mapping of genomes. The totality of all genetic material (deoxyribonucleic acid or DNA) in an organism is organized in a very precise way, though by no means fixed or constant. In the case of viruses, most of them will have ribonucleic acid or RNA as the genetic material.

Proteomics is the large-scale study of proteins, particularly their structures and functions. This term was coined to make an analogy with genomics, and while it is often viewed as the "next step" in bioinformatics, proteomics is more complicated than genomics. The genome is a constant entity, while the proteome differs from cell to cell, and changes constantly through its interactions with the genome and its environment. One organism has radically different protein expressions in different parts of its body, in different stages of its life cycle and in different environmental conditions.

Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is the "systematic study of the unique chemical fingerprints specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the collection of metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes (Daviss, 2005).

Classical bioinformatics

Most biologists use computers to store, compare, retrieve or analyze the structure of biomolecules. "Biomolecules" include human genetic material - nucleic acids - and the products of genes, or proteins. Nucleic acids and genetic proteins are central to "classical" bioinformatics, and integral to sequence analysis. In 1987, Hogeweg defined bioinformatics as "...the study of informatic processes in biotic systems". Tekaia at the French Institut Pasteur defined bioinformatics as "...the mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information."

New, applied bioinformatics

Without a doubt, our greatest achievement in bioinformatics is the Human Genome Project, the mapping of the human genome which was completed nearly 20 years ago. Although its priorities and future directions continue to change, in the post-genome medical era, many physicians believe that there is enormous potential for better medicines, targeted drugs and improved human health because of the human genome project. (See the frequently-asked questions at the National Human Genome Research Institute: What is a human genome?).

Here is some of the ongoing research as a result of the Human Genome project:

• Humans (& other species) have genomes that can be examined for differences/similarities; conclusions about evolution can be drawn from this data;

• the area is often called comparative genomics

• New technologies can measure the relative number of copies of a genetic message (levels of gene expression) at different stages of development or disease processes in different tissues;

• technologies such as DNA microarrays are growing in importance

• Large-scale ways of identifying gene functions and associations (for example, yeast two-hybrid methods) will grow in significance as will the accompanying bioinformatics of functional genomics.
• A shift in emphasis will occur from sequence analysis of genes to creating gene products;

• in turn, this will lead to:
  
• attempts to catalogue interactions between gene proteins, called proteomics.
• predicting structures of all human proteins - structural genomics.

Health library context - Canada

Academic health librarians across Canada take reference questions from bioinformaticians, and many have learned how to search and teach how to search the NCBI databases. While every health librarian knows how to search PubMed, few understand how to search for nucleotides or sequence information, the human genome or genetic mutations. Many academic health librarians prefer to increase their understanding of bioinformatics by searching the databases, and then extending their reach thereafter. The National Library of Medicine offers introductory courses for health librarians on searching the NCBI databases.

In 2009, CHLA/ABSC (Canada) offered a comprehensive course on bioinformatics for health librarians (see Kathy Hysen’s review of the course published in the JCHLA/JABSC). The course raised awareness of bioinformatics' issues for academic librarians. Natalie Clairoux at the Bibliothèque de la santé, Université de Montréal, has a background in bioinformatics, and has designed workshops on searching NCBI databases. Similar workshops are offered at York University's Steacie Library and the University of Calgary's Library where bioinformatics searching is integrated into some of its undergraduate courses (IFLA 2008). There are bioinformatics degree programs offered at UBC, although the library has yet to be formally involved in supporting them.

According to a 2010 survey by Dennie, one-quarter of health librarians in Canada provide some sort of service to support the study and practice of bioinformatics. However, individual consultations with students are rare; the libraries where bioinformatics services are offered are within university medical schools. Concordia's structural and functional genomics researchers use bioinformatics databases at least once a day; many faculty learn how to use these resources on their own and teach their students how to use them. However, Concordia faculty are also open to collaborations with librarians. The survey concluded that library services to support bioinformatics at Canadian universities are in an early phase of development. Health librarians can still be trained to use bioinformatics databases to help market the library to faculty and students.