Entrez Bioinformatics Databases and Tools : For Librarians

(1) Brown C. Where Do Molecular Biology Graduate Students Find Information? Science & Technology Libraries 2005;25(3):89-104. 10.1300/J122v25n03_06

(2) Geer RC. Broad issues to consider for library involvement in bioinformatics. Journal of the Medical Library Association 2006 July;94(3):286-298. PMID: 16888662

(3) Lyon J. Beyond the Literature: Bioinformatics Training for Medical Librarians. Med.Ref.Serv.Q. 2003 Spring;22(1):67-74. PMID: 12627692

(4) Yarfitz S, Ketchell DS. A library-based bioinformatics services program. Bull.Med.Libr.Assoc. 2000 January;88(1):36-48. PMID:10658962

RefShare Bibliography
A complete list of articles found through a literature search that may be helpful for librarians interested in bioinformatics (links to a RefShare account in RefWorks).

Allele

One of two or more versions of a gene. An individual inherits two alleles for each gene, one from each parent. If the two alleles are the same, the individual is homozygous for that gene. If the alleles are different, the individual is heterozygous. Though the term "allele" was originally used to describe variation among genes, it now also refers to variation among non-coding DNA sequences. (2)

Amino Acids

Set of 20 different molecules used to build proteins. Proteins consist of one or more chains of amino acids called polypeptides. The sequence of the amino acid chain causes the polypeptide to fold into a shape that is biologically active. The amino acid sequences of proteins are encoded in the genes. (2)

Base Sequence

The order of nucleotide bases in a DNA molecule; determines structure of proteins encoded by that DNA. (3)

Chromosome

An organized package of DNA found in the nucleus of the cell. Different organisms have different numbers of chromosomes. Humans have 23 pairs of chromosomes--22 pairs of numbered chromosomes, called autosomes, and one pair of sex chromosomes, X and Y. Each parent contributes one chromosome to each pair so that offspring get half of their chromosomes from their mother and half from their father. (2)

Domain

A discrete portion of a protein assumed to fold independently of the rest of the protein and which possesses its own Function. (1)

Enzyme

A biological catalyst and is almost always a protein. It speeds up the rate of a specific chemical reaction in the cell. The enzyme is not destroyed during the reaction and is used over and over. A cell contains thousands of different types of enzyme molecules, each specific to a particular chemical reaction. (2)

Exon

An exon is the portion of a gene that codes for amino acids. In the cells of plants and animals, most gene sequences are broken up by one or more DNA sequences called introns. The parts of the gene sequence that are expressed in the protein are called exons, because they are expressed, while the parts of the gene sequence that are not expressed in the protein are called introns, because they come in between--or interfere with--the exons. (2)

Gene

The basic physical unit of inheritance. Genes are passed from parents to offspring and contain the information needed to specify traits. Genes are arranged, one after another, on structures called chromosomes. A chromosome contains a single, long DNA molecule, only a portion of which corresponds to a single gene. Humans have approximately 23,000 genes arranged on their chromosomes. (2)

Genome

The entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the nucleus, as well as a small chromosome found in the cells' mitochondria. These chromosomes, taken together, contain approximately 3.1 billion bases of DNA sequence.Genotype

Genetic identity of an individual that does not show as outward characteristics. (1)

Intron

An intron is a portion of a gene that does not code for amino acids. In the cells of plants and animals, most gene sequences are broken up by one or more introns. The parts of the gene sequence that are expressed in the protein are called exons, because they are expressed, while the parts of the gene sequence that are not expressed in the protein are called introns, because they come in between the exons.

Locus (Loci)

A locus is the specific physical location of a gene or other DNA sequence on a chromosome, like a genetic street address. The plural of locus is "loci". (2)

mRNA

messenger RNA. mRNA describes the section of a genomic DNA sequence that is transcribed, and can include the 5' untranslated region (5'UTR), CDS, and 3' untranslated region (3'UTR). Successful translation of the CDS section of an mRNA results in the synthesis of a protein. (1)

Nucleic Acid

A class of macromolecules found in all cells and viruses. The functions of nucleic acids have to do with the storage and expression of genetic information. Deoxyribonucleic acid (DNA) encodes the information the cell needs to make proteins. A related type of nucleic acid, called ribonucleic acid (RNA), comes in different molecular forms that participate in protein synthesis. (2)

Nucleotide

The basic building block of nucleic acids. RNA and DNA are polymers made of long chains of nucleotides. A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base. The bases used in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T). In RNA, the base uracil (U) takes the place of thymine. (2)

Polymorphism

Polymorphism involves one of two or more variants of a particular DNA sequence. The most common type of polymorphism involves variation at a single base pair. Polymorphisms can also be much larger in size and involve long stretches of DNA. Scientists are studying how SNPs (single nucleotide polymorphisms, pronounced "snips")in the human genome correlate with disease, drug response, and other phenotypes. (2)

Protein

A class of molecules found in all living cells. A protein is composed of one or more long chains of amino acids, the sequence of which corresponds to the DNA sequence of the gene that encodes it. Proteins play a variety of roles in the cell, including structural (cytoskeleton), mechanical (muscle), biochemical (enzymes), and cell signaling (hormones). (2)

Ribosome

A cellular particle made of RNA and protein that serves as the site for protein synthesis in the cell. The ribosome reads the sequence of the messenger RNA (mRNA) and, using the genetic code, translates the sequence of RNA bases into a sequence of amino acids. (2)

Sources

1. NCBI Glossary. NCBI Handbook
2. Talking Glossary of Genetic Terms. NIH National Human Genome Research Institute.
3. Genome Glossary. US Department of Energy Human Genome Program.

Lyra Eugenio-Thomson is a graduate student in the School of Library and Information Studies at the University of Wisconsin-Madison.  The intent of this library guide is to gather helpful links for each of the bioinformatics genomic and molecular databases and data analysis tools offered in Entrez through NCBI. Lyra constructed this guide in Bioinformatics with the help of Emily Wixson who is the Reference and Instruction Librarian at the Chemistry Library.  This library guide fulfills the class practicum requirement for LIS 826 (Library and Information Literacy Instruction [LILI]).