Glossary

Abduction: A form of logical inference, commonly applied in the process of medical diagnosis. Given an observation, abduction generates all known causes. See also: Deduction, Induction, Inference.

Agent: Computer software constructed to operate with a degree of autonomy from its user, e.g. an agent may search the Internet for information based upon loose specifications provided by its user. See also: Artificial Intelligence.

Algorithm: A set of instructions to programmatically carry out some task. In clinical practice algorithms usually, but not always, involve some form of numerical calculation. See also: Protocol, Guideline, Care Pathway, Practice Parameter.

Allele: Variant form of the same gene.

Alphabet: The set of symbols that defines a particular language. See: Language.

Alternative Splicing Product: Variation in the way pre-mRNA is spliced together. Introns are typically spliced (removed) from pre-mRNA and the remaining exons are pieced together to form a contiguous transcript of mRNA (see Exon). However, the same set of introns may not always be spliced out, and the resultant mRNA may have a different combination of introns and exons. These alternative versions of the mRNA result in different downstream proteins being formed (alternative splicing products). Alternative splicing products are one reason why the number of gene products is much larger than the number of genes.

Annotation: The routine process of assignment of functions to genes in a sequenced genome or the extraction of biological knowledge from raw nucleotide sequences.

Antisense: Nucleic acid molecules that bind a complimentary strand of nucleic acid to modify gene expression.

Application: Synonym for a computer program that carries out a specific type of task. Word-processors or spreadsheets are common applications available on personal computers.

Arden syntax: A language created to encode actions within a clinical protocol into a set of situation-action rules, for computer interpretation, and also to facilitate exchange between different institutions.

ARPAnet: Advanced Research Projects network. A computer network developed by the United States Department of Defence in the late 1960s, and the forerunner of today’s Internet.

Artificial intelligence (AI): Any artefact, whether embodied solely in computer software, or a physical structure like a robot, that exhibits behaviours associated with human intelligence. Also the study of the science and methods for constructing such artefacts. See also: Turing test.

Artificial intelligence in medicine: The application of artificial intelligence methods to solve problems in medicine e.g. developing expert systems to assist with diagnosis, or therapy planning. See also: Artificial Intelligence, Expert system.

Assembly: construction of longer sequences, such as contigs or genomes, from shorter sequences, such as sequence reads with or without prior knowledge on the order of the reads or reference to a closely related sequence.

Asynchronous communication: A mode of communication between two parties, when the exchange does not require both to be active participant in the conversation at the same time e.g. sending a letter. See also: Synchronous communication, Isochronous communication Email.

ATM: Asynchronous Transfer Mode. A packet-based communication protocol that provides the high bandwidth transmission rates required for multimedia communication. See also: Packet-switched network, Circuit-switched network.

Augmented reality: The overlay of additional information onto human sense data e.g. overlaying labels onto images seen by a human.

Bandwidth: Amount of data that can be transmitted across a communication channel over a given period of time. See also, Bits per second, Channel capacity.

Base-pair (bp): Pair of complimentary nucleotides. Specific pairing of these bases (adenine with thymine and guanine with cytosine) forms the units of DNA and RNA that encode genetic information and facilitates accurate DNA replication. When quantified (e.g. 120bp), bp refers to the physical length of a sequence of nucleotides. (see DNA).

Bayes’ theorem: Theorem used to calculate the relative probability of an event given the probabilities of associated events. Used to calculate the probability of a disease given the frequencies of symptoms and signs within the disease and within the normal population. See also: Conditional probability, Prior Probability, Posterior Probability.

Bioinformatics: A sub-discipline of health informatics concerned with the application of molecular biology to biomedical science and translational medicine, especially the use of computational tools and algorithms in genomics and proteomics research. Historically, bioinformatics concerned itself with the analysis of the sequences of genes and their products (proteins), but the field has since expanded to the management, processing, analysis, and visualization of large quantities of data from genomics, proteomics, drug screening, and pharmacology.

Biomarker: A biological characteristic that is objectively measured and evaluated as an indicator of normal or pathological processes or host responses to a therapeutic intervention.

B-ISDN: Broadband ISDN. A set of communication system standards for ATM systems. See: ATM, ISDN.

Bit: One binary digit, in base 2. The basic unit for electronically stored or transmitted data. See also: Byte.

Bits per second: A measure of data transmission rate. See also: Bit.

BLAST (Basic logical alignment and search tool): A computer program for finding sequences in databases that have identity to a query sequence.

Bluetooth: Wireless communication system designed to allow many personal devices such as computers, mobile phones and digital cameras to communicate with each other over a short-range.

Boolean logic: A system of logic devised by Georges Boole that defined the meaning of linguistic notions like and, or and not to produce “laws of thought” which had a clear syntax and semantics.

Broadband network: General term for a computer network capable of high-bandwidth transmission rated. See also: ATM.

Browser: A program used to view data e.g. examining the contents of a database or knowledge base, or viewing documents on the World Wide Web. See also: Mosaic, World Wide Web, Internet.

Byte: Eight bits. Bytes are usually counted in kilobytes (1024 bytes), megabytes, and gigabytes. See also: Bit.

Candidate gene study: A study of specific genetic loci in which a phenotype-genotype association may exist (hypothesis-led genotype experiment).

Care Pathway: Describes the expected course of the patient’s management and what actions need to be taken at every stage. See also: Algorithm, Protocol, Guideline, Practice Parameter.

Case-based reasoning: An approach to computer reasoning that uses knowledge from a library of similar cases, rather than by accessing a knowledge base containing more generalised knowledge, such as a set of rules. See also: Artificial intelligence, Expert system.

Causal reasoning: A form of reasoning based on following from cause to effect, in contrast to other methods in which the connection is weaker, such as probabilistic association.

CDSS: Clinical Decision Support System.

Centrality: Family of social network metrics based on number or type of connections between an individual and others, to estimate degree of influence or location in the network.

CERN: Conseil Européan pour la Recherche Nucléaire. The European Particle Physics Laboratory. It was here that the initial set of standards were developed to create the World Wide Web. See: HTML, HTTP, WWW.

Channel: The connection between two parties that transports their messages, such as a telephone or email.

Channel capacity: Amount of data that can be transmitted per unit time along a communication channel. Synonym: Bandwidth.

Checklist: An ordered list of items that must be ‘ticked off’ as they are completed. See: Protocol.

Chromosome: One of the physically separate segments that together forms the genome, or total genetic material, of a cell. Chromosomes are long strands of genetic material, or DNA, that have been packaged and compressed by wrapping around proteins. The number and size of chromosomes varies from species to species. In humans, there are 23 pairs of chromosomes (a pair has one chromosome from each parent). One pair forms the sex chromosomes because they contain genes that determine sex. The chromosome carrying the male determining genes is designated Y and the corresponding female one is the X chromosome. The remaining pairs are called autosomes. Chromosome 1 is the largest and chromosome 22 the smallest. Each chromosome has two “arms” designated p and q.

Circuit-switched network: A communication network that connects parties by establishing a dedicated circuit between them. See also: Packet-switched network.

Client: A computer connected to a network that does not store all the data or software it uses, but retrieves it across the network from another computer that acts as a server. See also: Client-server architecture, Server.

Client-server architecture: A computer network architecture that places commonly used resources on centrally accessible server computers, which can be retrieved as they are needed across the network by client computers on the network. See also: Client, Server.

Closed-loop control: Completely automated system control method in which no part of the control system need be given over to humans. See also: Open-loop control.

Clustering: Algorithm that puts similar things together and different things apart.

Code: In medical terminological systems, the unique numerical identifier associated with a medical concept, which may be associated with a variety of terms, all with the same meaning. See also: Term.

Cognitive science: A multi-disciplinary field studying human cognitive processes, including their relationship to technologically embodied models of cognition. See also: Artificial Intelligence.

Communication protocol: The rules governing how a conversation may proceed between well-behaved agents. See also: OSI seven layer model.

Complementary DNA (cDNA): DNA that is synthesized from a messenger RNA template; the single-stranded form is often used as a probe in physical mapping or for detecting RNA. Since cDNA is constructed from messenger RNA (after introns have been spliced out), it does not contain introns.

Complex Adaptive System: A system characterized by high complexity and the ability to alter structure based upon a source of variation and a fitness function.

Complexity: The degree of connection between different component elements in a system.

Computer Network: For computers, any collection of computers connected together so that they are able to communicate, permitting the sharing of data or programs.

Computerised protocol: Clinical guideline or protocol stored on a computer system, so that it may be easily accessed or manipulated to support the delivery of care. See also: Clinical guideline.

Conditional probability: The probability that one event is true, given that another event is true. See: Bayes’ theorem.

Connectionism: The study of the theory and application of neural networks. See: Neural network.

Consent: Explicit agreement to allow another party to carry out an action on our behalf. See also: e-Consent.

Control system: A system that utilises measurement of its output and feedback to influence future behaviour based upon a measurement of past performance. See: System, Feedback, Cybernetics.

CPOE: Computerized Physician Order Entry. Clinical information system designed to support tasks such as ordering tests or medications.

CPR: Computer-based Patient Record. See: Electronic Health Record.

CSCW: Computer supported co-operative work. The study of computer systems developed to support groups of individuals work together. See also: Groupware.

Cybernetics: A name coined by Norbert Weiner in the 1950s to describe the study of feedback control systems and their application. Such systems were seen to exhibit properties associated with human intelligence and robotics, and so was an early contributory to the theory of artificial intelligence.

Cyberspace: Popular term now associated with the Internet, which describes the notional information “space” that is created across computer networks. See also: Virtual reality.

Data: Any and all complex data entities from observations, experiments, simulations, models and higher order assemblies, along with the associated documentation needed to describe and interpret them.

Data integration: The process of combining disparate data and providing a unified view of these data.

Data mining: Automatically searching large volumes of data for patterns or associations.

Data warehouse: An information infrastructure that enables researchers and clinicians to access and analyse detailed data and trends. Created by collecting databases and linking them using common data elements.

Database: A structured repository for data, consisting of a a collection of data and their associated data model, and usually stored on a computer system. The existence of a regular and formal indexing structure permits rapid retrieval of individual elements of the database. See also: Model, Knowledgebase.

Decision support system: General term for any computer application that enhances a human’s ability to make decisions.

Decision Tree: A method of representing knowledge which structures he elements of a decision into a tree-like fashion. Chance nodes in a decision tree represent alternative possibilities, and decision nodes represent alternative choices. The leaf nodes of the tree represent outcomes, which may be assigned a numerical utility. See also: Utility.

DECT: Digital European Cordless Telephony standard, which defines the architecture for wireless voice and data communication systems restricted to campus-size areas, rather than wide-area systems that would be publicly available.

Deduction. A method of logical inference. Given a cause, deduction infers all logical effects that might arise as a consequence. See also: Inference, Abduction, Induction.

Deoxyribonucleic Acid (DNA): The chemical that forms the basis of the genetic material in virtually all living organisms. Structurally, DNA is composed of two strands that intertwine to form a springlike structure called the double helix. Attached to each backbone are chemical structures called bases (or nucleotides), which protrude away from the backbone toward the centre of the helix, and which come in four types: adenine, cytosine, guanine, and thymine (designated A, C, G, and T). In DNA, cytosine only forms optimal hydrogen bonding with guanine, and adenine only with thymine. These interactions across the many nucleotides in each strand hold the two strands together.

Distributed computing: Term for computer systems in which data and programs are distributed across different computers on a network, and shared.

DNA sequencing: Biochemical methods for determining the order of the nucleotide bases, adenine, guanine, cytosine and thymine, in a DNA oligonucleotide.

DTMF: Dial Tone Multifrequency. The tones generated by punching in numbers on a telephone key-pad.

e-Consent: Explicit agreement from a patient to allow another party to view their data captured in an electronic health record. See also: Consent.

EDI: Electronic Data Interchange. General term describing the need for healthcare applications to be able to exchange data, requiring the adoption of agreed common standards for the form and content of the messages passing between applications. See also: HL7.

Electronic Health Record (EHR): A general term describing computer-based patient record systems. It is sometimes extended to include functions like order entry for medications and tests, amongst others. See also Electronic Medical Record, Electronic Nursing Record, Summary Care Record.

Electronic mail: See Email.

Electronic Medical Record (EMR): A general term describing computer-based patient record systems designed mainly for the use of doctors.

Electronic Nursing Record (ENR): A general term describing computer-based patient record systems designed mainly for the use of nurses.

Electrophoresis: The use of electrical fields to separate charged biomolecules such as DNA, RNA, and proteins. DNA and RNA carry a net negative charge because of the numerous phosphate groups in their structure. In the process of gel electrophoresis, these biomolecules are put into wells of a solid matrix typically made of an inert substance such as agarose. When this gel is placed into a bath and an electrical charge applied across the gel, the biomolecules migrate and separate according to size in proportion to the amount of charge they carry. The biomolecules can be stained for viewing and isolated and purified from the gels for further analysis. Electrophoresis can be used to isolate pure biomolecules from a mixture or to analyse biomolecules (such as for DNA sequencing).

Email: Electronic mail. Messaging system available on computer networks, providing users with personal mail-boxes from which electronic messages can be sent and received.

EMR: See: Electronic Medical Record.

Enzyme: A protein that catalyses chemical reactions in a living cell. Enzymes are protein molecules whose function it is to speed the making and breaking of chemical bonds required for essential physiochemical reactions.

Epigenetics: Heritable influence on gene activity that does not involve changes to the DNA sequence itself.

Epistemology: The philosophical study of knowledge.

Epitope: The regions of an antigen that bind to antigen-specific membrane receptors on lymphocytes.

EPR: Electronic Patient Record. See: Electronic Medical Record.

Evidence-based Medicine: A movement advocating the practice of medicine according to clinical guidelines, developed to reflect best-practice as captured from a meta-analysis of the clinical literature. See also: Clinical guideline, Meta-analysis, Protocol.

Exon: The protein-coding DNA sequences of a gene (see Intron).

Expected utility: In decision theory, the expected utility of a decision is the sum of the utilities of the same decision repeated over multiple trials. At the limit, with an infinite number of decisions, it is the sum of the utilities of each different possible outcome of that option, each weighted by its own probability. See also: Decision tree, utility.

Expected value: In probability theory, the expected value of variable is the sum of all its values over multiple trials. The expected value of the mean value of a normally distributed binary variable that can either be 0 or 1 is 0.5.

Expert system: A computer program that contains expert knowledge about a particular problem, often in the form of a set of if-then rules that is able to solve problems at a level equivalent or greater than human experts. See also: Artificial intelligence.

FAQ: Frequently Asked Questions. Common term for information lists available on the Internet, which has been compiled to newcomers to a particular subject, answering common questions that would otherwise often be asked by submitting email requests to a Newsgroup.

Feedback: Taking some or all of the output of a system and adding it to a system’s own input. See also: System.

Finite state machine: A knowledge representation that makes different states in a process explicit, and connects them with links that specify some transition condition that specifies how one traverses from one state to another.

Firewall: A security barrier erected between a public computer network like the Internet and a local private computer network.

First-principles, reasoning from: Use of a model of the mechanisms that control a system to predict or simulate the likely outcome if some of the inputs or internal structure of the system is altered. See also: System.

Fitness Landscape: A mathematical surface representing the relationship between phenotype and fitness for an organism, technology, organization or other construct existing within a complex adaptive system.

Formative assessment: Evaluation of the performance of an information system against user needs. See also: Summative assessment.

FTP: File Transfer Protocol. A computer protocol that allows electronic files to be sent and received in a uniform fashion across a computer network.

Functional genomics: Exploration of the function of genes and other parts of the genome.

Fuzzy logic: An Artificial intelligence method for representing and reasoning with imprecisely specified knowledge, for example defining loose boundaries to distinguish “low” from “high” values. See also: Qualitative reasoning, Artificial intelligence.

Gene: An ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product such as a protein.

Gene ontology: A set of controlled vocabularies in molecular function, biological process and cellular component for the standardised annotation of genes and gene products across all species.

Gene prediction (or gene calling): is the procedure of identifying protein and RNA sequences coded on the sample DNA.

Gene product: The biochemical material, either RNA or protein, resulting from expression of a gene. The amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles. As gene products include all the alternative splicing products, there are estimated to be at least 100,000 distinct such products.

Gene therapy: The technology that uses genetic material for therapeutic purposes. This genetic material can be in the form of a gene, representative of a gene or cDNA, RNA, or even a small fragment of a gene. The introduced genetic material can be therapeutic in several ways: It can make a protein that is defective or missing in the patient’s cells (as would be the case in a genetic disorder), or that will correct or modify a particular cellular function, or that elicits an immune response.

Genome: The complete set of genetic information in an organism. In bacteria, this includes the chromosome(s) and extrachromosomal genetic information, e.g. plasmids.

Genome-level characters: Features of a genome or its products other than the linear sequences of nucleotides or amino acids that can be assessed for phylogenetic analysis.

Genome-wide association study: A study in which genetics markers across the entire genome, such as Single Nucleotide Polymorphisms (SNPs), are searched for association with disease to pinpoint the genetic differences that correlate with and may therefore play a causative role in that disease (experiment without prior hypothesis).

Genomics: The study of the entire genome of an organisms; structural genomics includes whole-genome sequencing, whereas functional genomics aims to determine the functions of all genes.

Genotype: The entire genetic constitution of an organism or the genetic composition at a specific gene locus or set of loci.

Grammar: The set of rules that together specify the allowed ways an alphabet can be put together to forms strings of symbols in a given language. See: Alphabet, Language, Syntax.

Group: A group collects together a number of different codes associated with medical events that are considered to be sufficiently similar for some purpose e.g. the determination of an appropriate reimbursement for approximately similar clinical procedures or diseases. See also: Term, Code.

Groupware: A computer application that assists communication and shared working amongst groups of individuals with access to a common computer network, but who may be geographically or temporally separated. See also: CSCW.

GSM: The Global System of Mobility. A widely adopted international standard for the architecture and operation of digital cellular telephony systems that can carry voice and data circuits, as well as short packet-data messages.

GUI: Graphical User Interface. That part of a computer application seen and interacted with by its user. Specifically, that part of the interface that is based upon visual structures like icons, which act as metaphors for the different functions supported by the application e.g. deleting a file is enacted by dragging a visual symbol representing the file onto a trash can icon.

Guideline: An agreed set of steps to be taken in the management of a clinical condition. See also: Algorithm, Care Pathway, Practice Parameter, Protocol.

Hardware: For a computer system, all its physical components, as distinguished from the programs and data that are manipulated by the computer. See also: Software.

Health Information Exchange: A computer network designed to allow different clinical information systems to interconnect and share patient level data.

Heuristic: A rule of thumb that describes how things are commonly understood, without resorting to deeper or more formal knowledge. See also: Model-based reasoning.

HIS: Hospital information system. Typically used to describe hospital computer systems with functions like patient admission and discharge, order entry for laboratory tests or medications, and billing functions. See also: Electronic Medical Record.

HL7 (Health Level 7): An international standard for electronic data exchange in healthcare, which defines the format and content of messages that pass between medical applications.

Home page: A document on the World Wide Web that acts as a front page or point of welcome to a collection of documents that may introduce an individual, organisation, or point of interest.

Homeostasis: The use of feedback systems to keep a desired state. Often used to describe physiological steady-states. See also: Feedback.

Homophily: The preference for individuals to form social ties with others who share similar interests, beliefs, and behaviours. See: Social network.

Horizontal gene transfer: Any process in which an organism transfers genetic material to another cell that is not its offspring. This process is in contrast to more common vertical gene transfer, which occurs when genetic information is passed from parent to offspring

HTML: Hypertext Mark-up Language. The description language used to create hypertext documents that can be viewed on the World Wide Web. See also: HTTP, World Wide Web.

HTTP: Hypertext Transfer Protocol. Communication protocol used on the Internet for the transfer of HTML documents. See also: HTML, World Wide Web.

Human-computer interaction: The study of the psychology and design principles associated with the way humans interact with computer systems.

Human-computer interface: The “view” presented by a program to its user. Often literally a visual window that allows a program to be operated, an interface could just as easily be based on the recognition and synthesis of speech, or any other medium with which a human is able to sense or manipulate.

Hybridisation: The interaction of complementary nucleic acid strands. Since DNA is a double-stranded structure held together by complementary interactions (in which C always binds to G, and A to T), complementary strands favourably reanneal or “hybridise” to each other when separated.

Hyperlink: A connection between hypertext documents, that allows a reader to trace concepts appearing in one document to related occurrence in other documents.

Hypertext: A method of presenting documents electronically that allows them to be read in a richly interconnected way. Rather than following a single document from beginning to end, sections of each document are connected to related occurrences in other documents via hyperlinks, permitting “non-linear” reading following concepts of interest to the reader. See also: Hyperlink, HTML, World Wide Web.

ICD-9: The International Classification of Diseases, 9th edition. Published by World Health Organization.

ICD-10: The International Classification of Diseases, 10th edition. Published by World Health Organization.

Implementation: The act of fitting a technological construct such as an information system into a working setting such as an organization. Also the act of taking a design and translating it into a working system.

Implementation Science: The study of the process of implementation.

Indicator: A measureable event or quantity that can be used to monitor a system, such as progress of a disease or quality, efficiency or safety of a health service process.

Indifference probability: The probability at which a decision maker is indifferent to the present outcome (status quo) or taking a gamble that might improve or worsen the situation. Used to determine utilities in the standard gamble method. See also: Standard Gamble, Utility.

Induction: A method of logical inference used to suggest relationships from observations. This is the process of generalisation we use to create models of the world. See also: Deduction, Abduction, Inference.

Infectome: System of networks of interacting host and pathogen’s genes, proteins and metabolites involved in a process of infection and disease.

Inference: A logical conclusion drawn using one of several methods of reasoning, knowledge and data. See also: Abduction, Deduction, Induction.

Information superhighway: A popular term associated with the Internet, used to describe its role in the global mass transportation of information.

Information Theory: Initially developed by Claude Shannon, describes the amount of data that can be transmitted across a channel given specific encoding techniques and noise in the signal. See: Channel.

Internet: Technically, a network of computer networks. Today, associated with a specific global computer network which is publicly accessible, and upon which the World Wide Web is based. See also: ARPAnet, World Wide Web.

Intranet: A computer network, based upon World Wide Web and Internet technologies, but whose scope is limited to an organisation. An intranet may be connected to an Internet, so that there can be communication and flow of information between it and other intranets. See also: Internet, World Wide Web.

Intron: Noncoding portion of the gene that is spliced out from the nascent RNA transcript in the process of making an mRNA transcript. Frequently includes regulator elements (i.e. binding sites) in addition to those of the promoter.

IP (Internetworking Protocol): Communication protocol to allow different individual networks to communicate with each other. IP is the basis of the Internet’s communication infrastructure.

IP address: The address of a computer on the Internet, which permits it to send and receive messages from other computers on the Internet.

ISDN: Integrated Services Digital Network. A digital telephone network that is designed to provide channels for voice and data services.

Isochronous Communication: A communication process that operates at a regular interval to provide a certain minimum data rate e.g. sending a communication with a guaranteed regularity in ATM. See also: Synchronous communication, Asynchronous communication, ATM.

Knowledge acquisition: Sub-speciality of artificial intelligence, usually associated with developing methods for capturing human knowledge and of converting it into a form that can be used by computer. See also: Machine learning, Expert system, Heuristic.

Knowledge base: A structured repository for knowledge, consisting of a collection of knowledge elements such as rules and their associated data model, or Ontology. A knowledgebase is a core component of an Expert System. See also: Database, Model, Ontology, Expert System.

Knowledge based system: See: Expert system.

LAN: Local Area Network. A computer network limited to servicing computers in a small locality. See also: Intranet.

Language: A formal language specifies a way of constructing messages. A language is built from an alphabet of allowed symbols, which can be arranged according to rules, which define the syntax of the language. See: Grammar.

Machine learning: Sub-speciality of artificial intelligence concerned with developing methods for software to learn from experience, or to extract knowledge from examples in a database. See also: Artificial intelligence, Knowledge acquisition.

Mailing List: A list of email addresses for individuals. Used to distribute information to small groups of individuals, who may, for example, have shared interests. See also: Email.

Medline: Bibliographic database maintained by the National Library of Medicine in the US, that indexes articles published by most of the major biomedical journals.

Megabyte: 1,048,576 or 220 bytes. See: Byte.

Messenger RNA (mRNA): The RNA that codes for proteins and is active in the cellular cytoplasm.

Meta-analysis: A statistical method that pools the results from multiple similar experiments, hoping that the improved power obtained from the combined data sets will identify statistically significant patterns that cannot be identified within the smaller sample sizes of individual studies.

Metagenomics: The high-throughput study of sequences from multiple genomes recovered from samples that contain mixed microbial populations.

Microarray: A technology used ti study many genes at once. Hundreds of samples containing DNA or RNA are deposited as dots on the slide. The binding of complimentary base pairs from the sample and the gene sequences on the slide can be measured with the use of fluorescence.

Microbiome: Collective system of genomes of all microbial flora of the human.

Model: Any representation of a real object or phenomenon, or template for the creation of an object or phenomenon.

Model-based reasoning: Approach to the development of expert systems that uses formally defined models of systems, in contrast to more superficial rules of thumbs. See also Heuristic, Artificial intelligence.

Modem: Modulator-demodulator. Device used for converting a digital signal into tones that can be transmitted down a telephone wire.

Mosaic: The first commonly available World Wide Web browser for viewing hypertext documents, developed at CERN.

Multidimensional data: data spanning multiple levels or context of granularity or scope while maintaining one or more common linkages that span such levels.

Multimedia: Computer systems or applications that are able to manipulate data in multiple forms, including still and video images, sound and text.

Mutation: Any alteration to DNA that can potentially result in a change in the function of one or more genes. Mutations can be a change in a single base of DNA (point mutation) or a loss of base pairs (deletion) affecting a single gene, or a movement of chromosomal regions (translocation) affecting many genes. Some changes in DNA occur naturally and lead to no harmful effects; these changes in a population are called polymorphisms.

Network: Series of points or nodes interconnected by edges, edges can have direction or different weights.

Neural computing: see Connectionism.

Neural network: Computer program or system designed to mimic some aspects of neurone connections, including summation of action potentials, refractory periods and firing thresholds.

Newsgroup: A bulletin board service provided on a computer network like the Internet, where messages can be sent by email and be viewed by those who have an interest in the contents of a particular newsgroup. See also: Email, Internet.

Next-generation sequencing: Novel approaches to DNA sequencing that dispense with the need to create libraries of clones sequences in bacteria and provides faster and cheaper sequencing

Noise: Unwanted signal that is added to a transmitted message while being carried along a channel, and distorts the message for the receiver. See: channel.

Northern Blot: RNA from a sample is spatially separated and distributed by mass on a gel. Radioactively labelled DNA or RNA strands with sequence complementary to the RNA segments from the sample are used to locate the position of those RNA segments.

Object-oriented programming: Computer languages and programming philosophy that emphasises modularity amongst the elements of a program and their sharing of properties and intercommunication.

Oligonucleotide: A short molecule consisting of several linked nucleotides (typically between 10 and 60) chained together and attached by covalent bonds.

Ontology: A formal and rigorous description of the set of concepts entities within a body of knowledge and the relationships between them. An ontology can help reason about the entities by identifying legal and nonsense relationships and inferences. Usually represented as hierarchy, and often as a richly interconnected set of objects, concepts and other entities that embody knowledge about a given field. See also: Knowledge base, Language.

Open-loop control: Partially automated control method in which a part of the control system is given over to humans.

Open Reading Frame: Regions in a nucleotide sequence that are bounded by start and stop codons and are therefore possible gene coding regions.

Open system: Computer industry term for computer hardware and software that is built to common public standards, allowing purchasers to select components from a variety of vendors and use them together.

Orthologous: Homologous genes in two or more organisms that are related only by lineage splitting and not by gene duplication.

OSI seven layer model: International Organization for Standardization (ISO) model that defines the protocol layers for communicating between heterogeneous computers. See also: communication protocol.

PABX: Public Area Branch Exchange. Telecommunication network switching station that connects telephones in an area with the wider telephone network.

Packet-switched network: Computer network which exchanges messages between different computers not by seizing a dedicated circuit, but by sending a message in a number of uniformly sized packets along common channels, shared with other computers. See also: Circuit-switched network.

Pharmacogenomics: The study of the pharmacological response to a drug by a population based on the genetic variation of that population. It has long been known that different individuals in a population respond to the same drug differently, and that these variations are due to variations in the molecular receptors being affected by the drug, or to differences in metabolic enzymes that clear the drug. Pharmacogenomics is the science of studying these variations at the molecular level. Applications of pharmacogenomics include reducing side effects, customizing drugs, improvement of clinical trials, and the rescue of some drugs that have been banned due to severe side effects in a small percentage of the eligible population.

Personal Health Record: View of the electronic health record designed for patient’s, which also may include patient created records. See also: Electronic Health Record.

Phenotype: The observable traits of an individual person. Some traits are determined largely by genotype (e.g. blood type), whereas others (e.g. height) are determined by environmental factors.

Physician’s workstation: A computer system designed to support the clinical tasks of doctors. See also: Electronic Medical Record.

Polymerase chain reaction (PCR): A technique used to amplify or generate large amounts of replica DNA or a segment of any DNA whose “flanking” sequences are known. Oligonucleotide primers that bind these flanking sequences are used by an enzyme to copy the sequence in between the primers. Cycles of heat to break apart the DNA strands, cooling to allow the primers to bind, and heating again to allow the enzyme to copy the intervening sequence lead to doubling of the DNA present at each cycle.

Polymorphism: Common variation in a region of DNA sequence

Posterior probability: The probability that an event occurs with evidence both about the prior probability and also about the current case in question. See: Bayes’ theorem, Prior Probability.

Postscript: Commercial language that describes a common format for electronic documents that can be understood by printing devices and converted to paper documents or images on a screen.

Post-test probability: Posterior-probability of an event, after a test to see if the event is true. See: Posterior probability, Pre-test probability.

Practice parameter: See: Care Pathway.

Precision. The percent of elements correctly matching a given attribute, out of all the elements identified as matching by a procedure.

Pre-test probability: Prior-probability of an event, ahead of a test. See: Prior probability, Post-test probabilty.

Prior probability: The probability that an event occurs in a population, with no evidence about the current case in question. See: Bayes’ theorem.

Probe: Any biochemical agent that is labelled or tagged in some way so that it can be used to identify or isolate a gene, RNA, or protein. Typically refers to the immobilized specified nucleic acid in a detection system.

Proteomics: The study of the entire protein complement or “protein universe” of the cell. Mirroring genomics, proteomics aims to determine the entire suite of expressed proteins in a cell. This includes determining the number, level, and turnover of all expressed proteins, their sequence and any post-translational modifications to the sequence, and protein-protein and protein-other molecule interactions within the cell, across the cell membrane, and among (secreted) proteins.

Protocol: A set of instructions that describe the procedure to be followed when investigating a particular set of findings in a patient, or the method to be followed in the management of a given disease See also: Algorithm, Care Pathway, Checklist, Guideline, Practice Parameter.

PSTN: Public Switched Telephone Network, providing ordinary voice-based telephone services.

Qualitative reasoning: A sub-speciality of artificial intelligence concerned with inference and knowledge representation when knowledge is not precisely defined, e.g. “back of the envelope” calculations.

Randomised Controlled Trail (RCT): A form of scientific study that randomly allocates patients to either a group receiving a new treatment, or to a control group. If patients or scientists do not know which group patients are allocated to, the trial is a Randomised Blinded Controlled Trial. See also: Systematic Review.

Read codes: Medical terminology system, developed initially for primary care medicine in the UK. Subsequently enlarged and developed to capture medical concepts in a wide variety of situations. See also: Terminology.

Reading frame: the succession of codons determined by reading nucleotides in groups of three from a specific starting position.

Reasoning: A method of thinking. See also: Inference.

Representation: The method chosen to model a process or object for example a building may be represented as a physical scale model, drawing or photograph. See also: Reasoning, Syntax.

Ribonucleic Acid (RNA): RNA is generated from the DNA template in the nucleus of the cell through a process called transcription, and is then exported into the cell cytoplasm from the nucleus where it begins the process of protein synthesis.

Rule-based algorithm: An algorithmic procedure based on identified genotype pattern and represented as a set of propositional rules.

Rule-based expert system: See: Expert system.

Search engine: Computer program capable of seeking information on the World Wide Web (or indeed any large data base) based upon search criteria specified by a user. See also: World Wide Web.

Semantics: The meaning associated with a set of symbols in a given language, which is determined by the syntactic structure of the symbols, as well as knowledge captured in an interpretative model. See also: Syntax.

Sequence alignment: the comparison of two or more sequences by searching for a series of individual characters or patterns that are in the same order in the sequence.

Server: A computer on a network that stores commonly used resources such as data or programs, and makes these available on demand to clients on the network. See also: Client, Client-server architecture.

SGML: Standard General Mark-up Language. Document definition language used in printing, and used as the basis for the creation of HTML. See also: HTML.

Signal to noise ratio: Measure of the amount of noise that has been added to a message during transmission. See: channel, information theory.

Single nucleotide polymorphism (SNP): Sites in the genome where individual organisms differ in their DNA sequence, often by a single base, usually with very low population frequencies.

SNOMED: The Systematised Nomenclature of Human and Veterinary Medicine. A commercially available general medical terminology, initially developed for the classification of pathological specimens. See also: Terminology.

Social contagion: The transmission of behaviours or beliefs across a social network.

Social network: The collection of strong and weak ties that link individuals into a social group.

Social media: A software application designed to support interactions between a group of individuals, as well as manage the creation of new ties between individuals.

Socio-technical system: The system created when people and technology together interact in an organisation, emphasising that both the human social, as well as technological, features contribute to the overall behaviour of the system.

Software: Synonym for computer program. See also: Application.

Southern Blot: DNA from a sample is cut with restriction enzymes and the position of the fragments (e.g. on a gel) is determined by the fragment’s molecular weight. Complementary strands of radioactively labelled DNA are used to identify the position of the DNA fragments on the gel.

Standard Gamble: A method to get an individual to express a preference for an outcome where the value is unknown as a preference for a gamble where the value for the outcomes are known. See also: Indifference probability, utility.

Summary Care Record (SCR): A general term describing a high level view of the computer-based patient record, typically restricted to a small number of information items considered most useful in quickly gaining an overview of a patient’s health circumstance. See also: Electronic Health Record.

Summative assessment: Evaluation of an information system against formal functional metrics or organisational outcome measures. See also: Formative assessment.

Symbol: A representation that is used to signify a more complex concept. See: Model.

Synchronous communication: A mode of communication when two parties exchange messages across a communication channel at the same time, e.g. telephones. See also: Asynchronous communication, Isochronous communication.

Syntax: The rules of grammar that define the formal structure of a language. See also: Semantics.

System: A collection of component ideas, processes or objects which has an input and an output. See also: Feedback.

Systematic Review: A formal process for searching for and then summarising the evidence contained in scientific papers, to obtain an aggregate view. The review process uses statistical techniques to appropriately combine the individual statistical results of each paper, which ideally is a randomised trial. See also Randomised Controlled Trial.

Systematized Nomenclature of Medicine (SNOMED): A standard vocabulary system for medical databases; contains more than 144,000 terms and is available in at least two languages. Developed by the College of American Pathologists.

Telco: Abbreviation for telecommunication company.

Teleconsultation: Clinical consultation carried out using a telemedical service. See also: Telemedicine.

Telemedicine: The delivery of health care services between geographically separated individuals, using telecommunication systems e.g. video conferencing.

Term: In medical terminologies an agreed name for a medical condition or treatment. See also: Code, Terminology.

Terminal: A screen and keyboard system that provides access to a shared computer system e.g. a mainframe or mini computer. In contrast to computers on a modern network, terminals are not computers in their own right.

Terminology: A standard set of symbols or words used to describe the concepts, processes and objects of a given field of study. See also: Term.

Transcription: The synthesis of RNA from DNA.

Transcription Factor: A molecule, typically a protein, which binds to DNA binding sites with some regulatory role in transcription. The binding (or unbinding) of a transcription factor from a promoter eventually leads to a change of transcription activity in the gene controlled by that promoter.

Translation: The process of reading of sequence bases in messenger RNA in order to create a sequence of amino acids i.e. protein.

True negative rate (Specificity): The percent of elements correctly detected as not matching a given attribute by a procedure, out of all the possible non-matching elements.

True positive rate (Sensitivity): The percent of elements correctly detected as matching a given attribute by a procedure, out of all the possible correct elements.

Turing test: Proposed by Alan Turing, the test suggests that an artefact can be considered intelligent if its behaviour cannot be distinguished by humans from other humans in controlled circumstances. See also: Artificial intelligence.

Unified Medical Language System (UMLS): A comprehensive metavocabulary maintained by the National Library of Medicine which combines >100 individual standardised vocabularies. The UMLS is composed of the Metathesaurus, the Specialist Lexicon, and the Semantic Network. The largest component of the UMLS is Metathesaurus, which contains the term string, concept grouping of terms, and concept interrelationships.

Universal genetic code: a misnomer based on an earlier, incorrect belief that all genomes share the same code for specifying amino acids from triplets of nucleotides.

URL: Universal Resource Locator. The address for a document placed on the World Wide Web. See also: World Wide Web.

User interface: The view a user has of a computer program, usually understood to mean the visual look and feel of a program, but also extending to other modes of interaction, e.g. voice and touch.

Utility: A quantitative measure assigned to an outcome, expressing the preference for that outcome compared to others. See also: Decision tree.

Value of Information (VOI): The economic value that can be placed on receiving particular data prior to making a decision. VOI is sometimes measured as the difference between two outcomes measured as expected utilities. See also: Expected utility.

Virtual Reality: Computer simulated environment within which humans are able to interact in some manner that approximates interactions in the physical world.

Virulence factor: A protein or a gene that is required for a pathogen to cause disease.

Vocabulary: See Terminology.

Voicemail: Computer based telephone messaging system, capable of recording and storing messages, for later review or other processing e.g. forwarding to other users. See also: Email.

W3: See: World Wide Web.

WAN: Wide Area Network. Computer network extending beyond a local area such as a campus or office. See also: LAN.

Whole-genome shortgun sequencing: An approach to determine the sequence of a genome in which the genome is broken into numerous small fragments. These fragments are then assembled en masse. The individual sequences are assembled into larger sequences (known as contigs) that correspond to substantial portions of the genome.

Workaround: A routine, behaviour or process created to bypass or augment a design element of a pre-existing system.

World Wide Web: An easy-to-use hypertext document system developed for the Internet allowing users to access multimedia documents. See also: Internet, CERN, HTTP, HTML, URL.

WWW: See: World Wide Web.

 

© Enrico Coiera 1997 – 2014

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