Commonly used terms in the Biomedical Sciences:

[Taken from the New York State Center of Excellence in Bioinformatics & Life Sciences (CoE) Website]

Bioinformatics   Using computer technology to manage large amounts of biological data (e.g., genetic information) for research in areas such as molecular biology, genomics and proteomics; development of databases and software tools related to the Human Genome Project and designed to ultimately improve the delivery of patient care through a better understanding of human biology.

Biomedical Informatics   The science underlying the acquisition, maintenance, retrieval, and application of biomedical knowledge and information to improve individualized patient care, medical education, and health sciences research. Biomedical informatics is an intersection of the computer science, medicine, biology, and health care fields. The goals of biomedical informatics research focus on the search for new knowledge (basic research) and the use of knowledge towards practical ends (applications research).

Biotechnology   A very diverse area within life sciences that involves the use of living organisms or biological techniques to provide chemicals (e.g., drugs), food and services that meet the needs of humans. Common examples of biotechnology drug products include antibiotics for bacterial infections and insulin for diabetes.

Clinical Trials   An investigation in which the effectiveness and safety of new medications or treatments are tested. In the United States , all drugs must undergo three phases of clinical trials before being approved for general use.

Combinatorial Chemistry   A collection of chemical and computational technologies for synthesizing, simulating and testing molecules to create a 'library' of many different compounds, which can be used to improve the activity of a drug or decrease side effects and reduce the development time and costs for pharmaceutical products.

Diagnostics   The branch of medical science which deals with the classification of disease; commonly refers to testing techniques used to determine whether or not a specified disease is present in a human or other living organism (e.g., PSA test for prostate cancer detection).

Drug Discovery and Development   A multi-stage process that includes the initial identification of targets for new drugs, the discovery and documentation of new drug candidates, and the subsequent development and clinical trials evaluation of a drug before it becomes approved for general use.

Electronic health record (EHR) / Electronic medical record (EMR)   A digital repository of descriptions of a patient's medical conditions, the treatments administered and the outcomes obtained. Aggregations of such descriptions created by healthcare institutions. More information is available on the
Agency for Health Research and Quality (AHRQ) National Resource Center for Health Information Technology website.

Genetics   The scientific study of patterns of inheritance of specific traits; how particular qualities or traits are transmitted from parents to offspring.

Genomics   The study of genes and their function, which involves the building of proteins from the information encoded by DNA, in the context of the total genetic information (genome) of an organism . Genomics is stimulating the discovery of breakthrough health care products by revealing thousands of new biological targets for the development of drugs and by giving scientists innovative ways to design new drugs, vaccines and diagnostic tests.

High Performance Computing   A branch of computer science that concentrates on supercomputers, which are the fastest type of computers that use specialized applications requiring immense amounts of mathematical calculations; an example is the supercomputer at the Center for Computational Research (CCR) at University at Buffalo, which is designed for high performance computing demands in areas like bioinformatics.

Human Genome Project    An international study of the entire human genetic material, which included contributions from local Roswell Park Cancer Institute Researchers who helped to identify the human DNA sequence (genes) in total; knowing the building blocks of humans will contribute to the understanding of disease and health processes and ultimately allow patient care to be delivered at the level of an individual's genetic makeup.

Immunology   The study of the body's immune system or natural defense mechanisms against disease.

Immunotherapy    A therapy that attempts to modify or enhance immune response, or reconstitute a damaged immune system by stimulating the body's own immune system. Research areas include finding treatments for cancer and HIV.

Medical Devices   an instrument, apparatus, implement, machine, implant, or other similar or related article, including a component part, or accessory which is intended for use in the diagnosis, prevention or treatment of health conditions. Medical devices range from simple tongue depressors and bedpans to complex programmable pacemakers with micro-chip technology and laser surgical devices, as well as including in vitro diagnostic products, such as general purpose lab equipment, reagents, and test kits.

Medical Informatics   A scientific field focused on the development of software applications (e.g., electronic medical records, automated health education) that improve health and wellness and the quality of care by facilitating tailored health communications and the diagnosis, treatment and management of patient health; use of information management technology to overcome the limitations of traditional methods for gathering, recording, storing, managing and communicating health information.

Molecular Biology   The study of the biochemical and molecular processes within cells.

Neurology   The scientific study of the nervous system, the bodily system made up of the brain and spinal cord. Specialists in this area treat such disorders as seizures, developmental delay, neuromuscular diseases, and severe or complicated language/learning disabilities.

Oncology   The branch of science that deals with the physical, chemical and biological properties and features of cancer, including the causes and progression of the disease.

Ontology   A structured representation of the types of entities and relations existing in a given domain that is designed to support exchange and reuse of data and information. Ontologies are used in biomedical informatics to support automatic retrieval and exchange of data across disciplinary boundaries.

*Ontology (Philosophical)   A branch of Western philosophy having its origins in ancient Greece in the work of philosophers such as Parmenides, Heraclitus, Plato, and Aristotle. Philosophical ontology is concerned with the study of what is, of the kinds and structures of objects, properties, events, processes, and relations in every area of reality. The term ‘ontology’ derives from the Greek ‘ontos’ (‘being’ or ‘what exists’) and ‘logos’ (‘rational account’ or ‘knowledge’). From the philosophical perspective, ‘ontology’ is synonymous with ‘metaphysics’ as classically conceived. This philosophical sense of the term is what Jacob Lorhard had in mind when he coined the term ‘ontology’ (ontologia) around 1613, and this is also why Nathan Bailey’s 1721 Oxford English Dictionary defined ontology as ‘an Account of being in the Abstract’.

*Ontology (Domain)   A representation of the things that exist within a particular domain of reality such as medicine, geography, ecology, or law, as opposed to philosophical ontology, which has all of reality as its subject matter. A domain ontology provides a controlled, structured vocabulary to annotate data in order to make it more easily searchable by human beings and processable by computers. The Gene Ontology Project is an example of a domain ontology that attempts to provide a taxonomy and controlled vocabulary for genes and gene products. Domain ontologies benefit from research in formal ontology, which assists in making communication between and among ontologies possible by providing a common language and common formal framework for reasoning.

*Ontology (Formal)   A discipline which assists in making communication between and among domain ontologies possible by providing a common language and common formal framework for reasoning. This communication is accomplished by (at least) the adoption of a set of basic categories of objects, discerning what kinds of entities fall within each of these categories of objects, and determining what relationships hold within and amongst the different categories in the domain ontology. Formal ontology draws heavily from the logic and methodology of philosophical ontology. Formal ontology is increasingly being applied in bioinformatics, intelligence analysis, management science, and in other scientific and business fields, where it serves as a basis for the improvement of classification, information organization, and automatic reasoning.

(* denotes ontology terms added by Robert Arp,

Personalized Medicine   Management of a patient's medical condition on the basis of the use of diagnostic tools employing molecular analysis of the patient's genome to achieve the optimal medical outcomes for that individual.

Pharmacology   Pharmacology is the science of the properties of drugs and their effects on the body.

Pharmacogenomics   The study of the interaction of an individual's genetic makeup and response to a drug.

Photodynamic Therapy   A type of cancer treatment that uses the interaction between laser light and a substance that makes cells more sensitive to light and in turn causes a chemical reaction that destroys the cancer cells.

Photonics   Technology of generating and harnessing light and other forms of radiant energy. The range of applications extends from energy generation, modulation and detection, and from information storage, processing and communications. Photonics incorporates the fields of optics, electrical engineering, physics, chemistry and materials science.

Proteomics   The study and cataloging of proteins in an organism in order to determine how they interact with each other. Researchers believe that this may hold the keys to curing diseases in humans and identifying targets for drug development.

Structural Biology   The study of the three-dimensional structure of molecules, such as proteins, and their interactions, as a way to understand how they function; facilitates the understanding and development of treatments for various diseases.

Systems Biology   The study of the interactions between components of biological systems and of how these interactions give rise to the behavior of the system and to the functions of its constituents.

Translational Medicine   A branch of medical research which seeks to draw inferences from research in basic biomedical sciences such as molecular and cell biology that are of significance for patient care.

The ORG's Usage of the term 'Ontology'

In line with the definition put forward by Barry Smith, Waclaw Kusnierczyk, Daniel Schober, and Werner Ceusters in the article titled,

"Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain",

the ORG uses the term in the following way:

An ontology is a representational artifact, comprising a taxonomy as proper part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them.

A REALISM-BASED ONTOLOGY is built out of representational units which are intended to refer exclusively to universals, and corresponds to that part of the content of a scientific theory that is captured by its constituent general terms and the interrelations between the universals denoted by these terms.

See the Glossary entry for 'Ontology' below.

Other Ontology Resources



  • National Center for Biomedical Ontology

  • National Center for Ontological Research

  • OBO Foundry Project

  • Ontology Outreach Advisory

  • The University at Buffalo



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