Bioinformatics definition

November 5, 2018 Off By admin

Bioinformatics Definition

Review on bioinformatics definition-Person view, organization view, and from other website sources

Keyword: Bioinformatics
Synonyms: Related: Computational Biology, Computational Molecular Biology, Biocomputing

Bioinformatics Definition -General view

Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine.

Roughly, bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; bioinformatics to them is a synonym for “computational molecular biology”- the use of computers to characterize the molecular components of living things.

Bioinformatics Definition -Personal view

The Tight Definition
“Classical” bioinformatics:
Fredj Tekaia at the Institut Pasteur offers this definition of bioinformatics:
“The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.

The Loose definition
There are other fields-for example medical imaging / image analysis which might be considered part of bioinformatics. There is also a whole other discipline of biologically-inspired computation; genetic algorithms, AI, neural networks. Often these areas interact in strange ways. Neural networks, inspired by crude models of the functioning of nerve cells in the brain, are used in a program called PHD to predict, surprisingly accurately, the secondary structures of proteins from their primary sequences. What almost all bioinformatics has in common is the processing of large amounts of biologically-derived information, whether DNA sequences or breast X-rays.

” Richard Durbin”, Head of Informatics at the Wellcome Trust Sanger Institute , expressed an interesting opinion : “I do not think all biological computing is bioinformatics, e.g. mathematical modelling is not bioinformatics, even when connected with biology-related problems. In my opinion, bioinformatics has to do with management and the subsequent use of biological information, particular genetic information.”

Bioinformatics definition – Organization / commitee

Bioinformatics definition by bioinformatics definition Committee, National Institute of Mental Health released on July 17, 2000 (source:

http://www.bisti.nih.gov/ ) (1)

The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no definition could completely eliminate overlap with other activities or preclude variations in interpretation by different individuals and organizations.

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data,including those to acquire, store, organize, archive, analyze, or visualize such data.

Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniquesto the study of biological, behavioral, and social systems.

The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as

“Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline.There are three important sub-disciplines within bioinformatics: the development of new algorithms and statistics with which to assess relationships among members of large data sets; the analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures; and the development and implementation of tools that enable efficient access and management of different types of information.” (2)

Bioinformatics- Definition (As submitted to the Oxford English Dictionary)

(Molecular) bio informatics: bioinformatics is conceptualising biology in terms of molecules (in the sense of Physical chemistry) and applying informatics techniques(derived from disciplinessuch as applied maths, computer science and statistics) to understand andorganise the information associatedwith these molecules, on a large scale. Inshort, bioinformatics is a managementinformation system for molecular biology and has many practical applications. (3)

(Source: What is bioinformatics? A proposed definition and overview of the field. NM Luscombe, D Greenbaum, M Gerstein (2001) Methods Inf Med 40: 346-58)

Bioinformatics definition – Website / other sources

Bioinformatics or computational biology is the use of mathematical and informational techniques, including statistics, to solve biological problems, usually by creating or using computer programs, mathematical models or both. One of the main areas of bioinformatics is the data mining and analysis of the data gathered by the various genome projects. Other areas are sequence alignment, protein structure prediction, systems biology, protein-protein interactions and virtual evolution.
(source: www.answers.com)
Bioinformatics is the science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research. (source: www.whatis.com)
As a discipline that builds upon computational biology, bioinformatics encompasses the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.
As a discipline that builds upon the life, health, and medical sciences, bioinformatics supports medical informatics; gene mapping in pedigrees and population studies; functional-, structural-, and pharmaco-genomics; proteomics, and dozens of other evolving ï¿½ï¿½omics.ï¿½
As a discipline that builds upon the basic sciences, bioinformatics depends on a strong foundation of chemistry, biochemistry, biophysics, biology, genetics, and molecular biology which allows interpretation of biological data in a meaningful context.
As a discipline whose core is mathematics and statistics, bioinformatics applies these fields in ways that provide insight to make the vast, diverse, and complex life sciences data more understandable and useful, to uncover new biological insights, and to provide new perspectives to discern unifying principles. In short, bioinformaticists bring a multidisciplinary perspective to many of the critical problems facing the health-science profession today.
“Biologists using computers, or the other way around. Bioinformatics is more of a tool than a discipline.(source: An Understandable Definition of Bioinformatics , The O’Reilly Bioinformatics Technology Conference, 2003) (4)
The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research.(source: Webopedia)
Bioinformatics: a combination of Computer Science, Information Technology and Genetics to determine and analyze genetic information. (Definition from BitsJournal.com)
Bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyse and merge biological data.(EBI – 2can resource)

Even though the three terms: bioinformatics , computational biology and bioinformation infrastructure are often times used interchangeably, broadly, the three may be defined as follows:

bioinformatics refers to database-like activities, involving persistent sets of data that are maintained in a consistent state over essentially indefinite periods of time;
computational biology encompasses the use of algorithmic tools to facilitate biological analyses; while
bioinformation infrastructure comprises the entire collective of information management systems, analysis tools and communication networks supporting biology.Thus, the latter may be viewed as a computational scaffold of the former two.

Bioinformatics is currently defined as the study of information content and information flow in biological systems and processes. It has evolved to serve as the bridge between observations (data) in diverse biologically-related disciplines and the derivations of understanding (information) about how the systems or processes function, and subsequently the application (knowledge). A more pragmatic definition in the case of diseases is the understanding of dysfunction (diagnostics) and the subsequent applications of the knowledge for therapeutics and prognosis.

Confusion over the Definition of “Bioinformatics” (2001)

An issue that regularly pops up is the definition of bioinformatics, particularly from individuals who are trying to get into the field. Most lament that there are too many definitions of bioinformatics.

This should be taken as an indication of the ubiquity of the subject. Bioinformatics, as both an enabling and enabled technology, will be defined differently depending on the domain of the person who is giving the definition. A computer scientist will give one definition, a biologist another, a biotechnologist yet another, and an individual from a pharmaceutical company will provide yet another definition.Each definition is as good as the other. This is just the nature of the beast.

A Bioinformaticist versus a Bioinformatician (1999)
Bioinformatics has become a mainstay of genomics, proteomics, and all other *.omics (such as phenomics) that many information technology companies have entered the business or are considering entering the business, creating an IT (information technology) and BT (biotechnology) convergence.

In almost all discussions and interviews, it became extremely clear that a distinction has to be made between a bioinformaticist and a bioinformatician.
A bioinformaticist is an expert who not only knows how to use bioinformatics tools, but also knows how to write interfaces for effective use of the tools.
A bioinformatician , on the other hand, is a trained individual who only knows to use bioinformatics tools without a deeper understanding.
Thus, a bioinformaticist is to *.omics as a mechanical engineer is to an automobile. A bioinformatician is to *.omics as a technician is to an automobile.

It has been argued that the professional categorization of bioinformatician and bioinformaticist may lead to some confusion. It is undeniable this may be the case. For example, a mathematician is an expert. However, we note that a physicist is an expert, so is a physician, except that they are in very different professions.

Definitions of Fields Related to Bioinformatics

Bioinformatics has various applications in research in medicine, biotechnology, agriculture etc. Following research fields has integral component of Bioinformatics

Computational Biology: The development and application of data-analytical andtheoretical methods, mathematical modeling and computational simulation techniquesto the study of biological, behavioral, and social systems.
Genomics: Genomics is any attempt to analyze or compare the entire genetic complement of a species or species (plural). It is, of course possible to compare genomes by comparing more-or-less representative subsets of genes within genomes.
Proteomics: Proteomics is the study of proteins – their location, structure and function. It is the identification, characterization and quantification of all proteins involved in a particular pathway, organelle, cell, tissue, organ or organism that can be studied in concert to provide accurate and comprehensive data about that system.
Proteomics is the study of the function of all expressed proteins. The study of the proteome, called proteomics, now evokes not only all the proteins in any given cell, but also the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins and their higher-order complexes, and for that matter almost everything ‘post-genomic’.” (5)
Pharmacogenomics : Pharmacogenomics is the application of genomic approaches and technologies to the identification of drug targets. In Short, pharmacogenomics is using genetic information to predict whether a drug will help make a patient well or sick. It Studies how genes influence the response of humans to drugs, from the population to the molecular level.
Pharmacogenetics: Pharmacogenetics is the study of how the actions of and reactions to drugs vary with the patient’s genes. All individuals respond differently to drug treatments; some positively, others with little obvious change in their conditions and yet others with side effects or allergic reactions. Much of this variation is known to have a genetic basis. Pharmacogenetics is a subset of pharmacogenomics which uses genomic/bioinformatic methods to identify genomic correlates, for example SNPs (Single Nucleotide Polymorphisms), characteristic of particular patient response profiles and use those markers to inform the administration and development of therapies. Strikingly such approaches have been used to “resurrect” drugs thought previously to be ineffective, but subsequently found to work with in subset of patients or in optimizing the doses of chemotherapy for particular patients.
Cheminformatics: ‘The mixing of those information resources [information technology and information management] to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization.’ (Frank K Brown ‘Chemoinformatics: what is it and how does it impact drug discovery.’ Ann. Rep. Med. Chem. 1998, 33 , 375-384.) (6)
Related terms of cheminformatics are chemi-informatics, chemometrics, computational chemistry, chemical informatics, chemical information management/science, and cheminformatics.
But we can distinguish chemoinformatics and chemical informatics as follows
Chemical informatics : ‘Computer-assisted storage, retrieval and analysis of chemical information, from data to chemical knowledge.’ ( Chem. Inf. Lett. 2003, 6 , 14.) This definition is distinct from ‘ Chemoinformatics ‘ (and the synonymous cheminformatics and chemiinformatics) which focus on drug design.
chemometrics: The application of statistics to the analysis of chemical data (from organic, analytical or medicinal chemistry) and design of chemical experiments and simulations. [IUPAC Computational]
computational chemistry : A discipline using mathematical methods for the calculation of molecular properties or for the simulation of molecular behavior. It also includes, e.g., synthesis planning, database searching, combinatorial library manipulation (Hopfinger, 1981; Ugi et al., 1990). [IUPAC Computational]
Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins , using computational tools and theoretical frameworks. One of the goals of structural genomics is the extension of idea of genomics , to obtain accurate three-dimensional structural models for all known protein families, protein domains or protein folds . Structural alignment is a tool of structural genomics.
Comparative genomics: The study of human genetics by comparisons with model organisms such as mice, the fruit fly, and the bacterium E. coli .
Biophysics:The British Biophysical Society defines biophysics as: “an interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function”.
Biomedical informatics / Medical informatics: “Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information.”
Mathematical Biology: Mathematical biology also tackles biological problems, but the methods it uses to tackle them need not be numerical and need not be implemented in software or hardware. It includes things of theoretical interest which are not necessarily algorithmic, not necessarily molecular in nature, and are not necessarily useful in analyzing collected data.
Computational chemistry: Computational chemistry is the branch of theoretical chemistry whose major goals are to create efficient computer programs that calculate the properties of molecules (such as total energy, dipole moment, vibrational frequencies) and to apply these programs to concrete chemical objects. It is also sometimes used to cover the areas of overlap between computer science and chemistry.
Functional genomics: Functional genomics is a field of molecular biology that is attempting to make use of the vast wealth of data produced by genome sequencing projects to describe genome function. Functional genomics uses high-throuput techniques like DNA microarrays, proteomics, metabolomics and mutation analysis to describe the function and interactions of genes.
Pharmacoinformatics: Pharmacoinformatics concentrates on the aspects of bioinformatics dealing with drug discovery
In silico ADME-Tox Prediction:(Brief description)- Drug discovery is a complex and risky treasure hunt to find the most efficacious molecule which do not have toxic effects but at the same time have desired pharmacokinetic profile. The hunt starts when the researchers look for the binding affinity of the molecule to its target. Huge amount of research requires to be done to come out with a molecule which has the reliable binding profile. Once the molecules have been identified, as per the traditional methodologies, the molecule is further subjected to optimization with the aim of improving efficacy. The molecules which show better binding is then evaluated for its toxicity and pharmacokinetic profiles. It is at this stage that most of the candidates fail in the race to become a successful drug.
Agroinformatics / Agricultural informatics: Agroinformatics concentrates on the aspects of bioinformatics dealing with plant genomes.
Systems biology:Systems biology is the coordinated study of biological systems by investigating the components of cellular networks and their interactions,by applying exprerimental high-throughput and whole-genome techniques, and integrating computational methods with experiemntal efforts.