In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of terms and relational expressions that represent the entities in that subject area. The field which studies ontologies so conceived is sometimes referred to as applied ontology.
Description logics (DL) are a family of formal knowledge representation languages. Many DLs are more expressive than propositional logic but less expressive than first-order logic. In contrast to the latter, the core reasoning problems for DLs are (usually) decidable, and efficient decision procedures have been designed and implemented for these problems. There are general, spatial, temporal, spatiotemporal, and fuzzy description logics, and each description logic features a different balance between expressive power and reasoning complexity by supporting different sets of mathematical constructors.
OpenGALEN is a not-for-profit organisation that provides an open source medical terminology. This terminology is written in a formal language called GRAIL and also distributed in OWL.
A clinical terminology server is a terminology server, which contains and provides access to clinical terminology.
The Unified Medical Language System (UMLS) is a compendium of many controlled vocabularies in the biomedical sciences. It provides a mapping structure among these vocabularies and thus allows one to translate among the various terminology systems; it may also be viewed as a comprehensive thesaurus and ontology of biomedical concepts. UMLS further provides facilities for natural language processing. It is intended to be used mainly by developers of systems in medical informatics.
The Systematized Nomenclature of Medicine (SNOMED) is a systematic, computer-processable collection of medical terms, in human and veterinary medicine, to provide codes, terms, synonyms and definitions which cover anatomy, diseases, findings, procedures, microorganisms, substances, etc. It allows a consistent way to index, store, retrieve, and aggregate medical data across specialties and sites of care. Although now international, SNOMED was started in the U.S. by the College of American Pathologists (CAP) in 1973 and revised into the 1990s. In 2002 CAP's SNOMED Reference Terminology was merged with, and expanded by, the National Health Service's Clinical Terms Version 3 to produce SNOMED CT.
Biomedical text mining refers to the methods and study of how text mining may be applied to texts and literature of the biomedical domain. As a field of research, biomedical text mining incorporates ideas from natural language processing, bioinformatics, medical informatics and computational linguistics. The strategies in this field have been applied to the biomedical literature available through services such as PubMed.
SNOMED CT or SNOMED Clinical Terms is a systematically organized computer-processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. SNOMED CT is considered to be the most comprehensive, multilingual clinical healthcare terminology in the world. The primary purpose of SNOMED CT is to encode the meanings that are used in health information and to support the effective clinical recording of data with the aim of improving patient care. SNOMED CT provides the core general terminology for electronic health records. SNOMED CT comprehensive coverage includes: clinical findings, symptoms, diagnoses, procedures, body structures, organisms and other etiologies, substances, pharmaceuticals, devices and specimens.
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people who build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.
Carole Anne Goble, is a British academic who is Professor of Computer Science at the University of Manchester. She is principal investigator (PI) of the myGrid, BioCatalogue and myExperiment projects and co-leads the Information Management Group (IMG) with Norman Paton.
Robert David Stevens is a professor of bio-health informatics. and former Head of Department of Computer Science at The University of Manchester
Frank van Harmelen is a Dutch computer scientist and professor in Knowledge Representation & Reasoning in the AI department at the Vrije Universiteit Amsterdam. He was scientific director of the LarKC project (2008-2011), "aiming to develop the Large Knowledge Collider, a platform for very large scale semantic web reasoning."
Basic Formal Ontology (BFO) is a top-level ontology developed by Barry Smith and his associates for the purposes of promoting interoperability among domain ontologies built in its terms through a process of downward population. A guide to building BFO-conformant domain ontologies was published by MIT Press in 2015.
In computer science, information science and systems engineering, ontology engineering is a field which studies the methods and methodologies for building ontologies, which encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities of a given domain of interest. In a broader sense, this field also includes a knowledge construction of the domain using formal ontology representations such as OWL/RDF. A large-scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering. Ontology engineering is one of the areas of applied ontology, and can be seen as an application of philosophical ontology. Core ideas and objectives of ontology engineering are also central in conceptual modeling.
The Disease Ontology (DO) is a formal ontology of human disease. The Disease Ontology project is hosted at the Institute for Genome Sciences at the University of Maryland School of Medicine.
Lawrence E. Hunter is a Professor and Director of the Center for Computational Pharmacology and of the Computational Bioscience Program at the University of Colorado School of Medicine and Professor of Computer Science at the University of Colorado Boulder. He is an internationally known scholar, focused on computational biology, knowledge-driven extraction of information from the primary biomedical literature, the semantic integration of knowledge resources in molecular biology, and the use of knowledge in the analysis of high-throughput data, as well as for his foundational work in computational biology, which led to the genesis of the major professional organization in the field and two international conferences.
Dipak Kalra is President of the European Institute for Health Records and of the European Institute for Innovation through Health Data. He undertakes international research and standards development, and advises on adoption strategies, relating to Electronic Health Records.
Betsy L. Humphreys is an American medical librarian and health informatician known for leading the cross-institutional efforts to establish biomedical terminology standards such as SNOMED CT and the Unified Medical Language System. She was the deputy director of the National Library of Medicine from 2005 until her retirement in 2017, serving as acting director from 2015 to 2016.
Mark Alan Musen is a Professor of Biomedical Informatics and of Biomedical Data Science at Stanford University, and Division Director of the Stanford Center for Biomedical Informatics Research. Musen's research focuses on open science, data stewardship, intelligent systems, and biomedical decision support. Since the late 1980s, Musen has led the development of Protégé, which is currently the most "widely used domain-independent, freely available, platform-independent technology for developing and managing terminologies, ontologies, and knowledge bases" in a range of application domains.
Morris Frank Collen was founder of the Kaiser Permanente Division of Research and an original member of the Permanente Medical Group, pioneering developer of Automated Multiphasic Health Testing (AMHT) systems, and Electronic Health Records (EHRs) for Public Health and Clinical Screening, serving as a model for pre-paid healthcare at the national level. Collen was a Founder of the American College of Medical Informatics (ACMI) in 1984, and the American Medical Informatics Association (AMIA) in 1989. The Morris F. Collen Award of Excellence was established in his honor by ACMI in 1993. In 1971 Collen was elected a member of the Institute of Medicine of the National Academy of Sciences.
