Strengths and limitations of formal ontologies in the biomedical domain.

Revista electrônica de comunicação, informação & inovação em saúde : RECIIS
Stefan SchulzBarry Smith

Abstract

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology of different kinds of logical resources, with a focus on description logics.The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals.We advocate a clear distinction of the four kinds of representation in order to provide a more rational basis for using of ontologies and related artifacts to advance integration of data and interoperability of associated reasoning systems.We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies when the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models.

Citations

Aug 13, 2010·Journal of Medical Systems·Vahid Jalali, Mohammad Reza Matash Borujerdi
May 4, 2011·Journal of Medical Systems·Alejandro Rodríguez-GonzálezAngel García-Crespo
Nov 28, 2012·Computers in Biology and Medicine·Alejandro Rodríguez-González, Giner Alor-Hernández
Sep 3, 2010·BMC Bioinformatics·Robert HoehndorfHeinrich Herre
Aug 13, 2011·BMC Systems Biology·Robert HoehndorfGeorgios V Gkoutos
Oct 15, 2011·Journal of Biomedical Semantics·Heinrich HerreStefan Schulz
Oct 29, 2013·International Journal of Medical Informatics·Bernd BlobelMathias Brochhausen
Apr 24, 2007·BMC Bioinformatics·Stefan SchulzUdo Hahn
May 23, 2012·Methods of Information in Medicine·A PugetJ F Brinkley
Aug 9, 2019·Database : the Journal of Biological Databases and Curation·Lars VogtPeter Grobe
Sep 3, 2021·International Journal of Medical Informatics·Jan FlorinCatrin Björvell

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.