CUILESS2016: a clinical corpus applying compositional normalization of text mentions

Journal of Biomedical Semantics
John D OsborneSteven J Bethard

Abstract

Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text. We annotated 5397 disorder mentions from the ShARe corpus to SNOMED CT that were previously normalized as "CUI-less" in the "SemEval-2015 Task 14" shared task because they lacked a pre-coordinated mapping. Unlike the previous normalization method, we do not restrict concept mappings to a particular set of the Unified Medical Language System (UMLS) semantic types and allow normalization to occur to multiple UMLS Concept Unique Identifiers (CUIs). We computed annotator agreement and assessed semantic coverage with this method. We generated the largest clinical text normalization corpus to date with mappings...Continue Reading

References

Oct 1, 1994·Computer Methods and Programs in Biomedicine·A L Rector, W A Nowlan
Feb 7, 1998·Journal of the American Medical Informatics Association : JAMIA·N R Hardiker, A L Rector
May 5, 2006·Protein Science : a Publication of the Protein Society·Karin VerspoorCliff Joslyn
Apr 27, 2007·Journal of the American Medical Informatics Association : JAMIA·James E AndrewsJeffrey Krischer
Jan 8, 2014·Journal of Biomedical Informatics·Rezarta Islamaj DoğanZhiyong Lu
Jun 3, 2014·BMC Bioinformatics·Rachael P HuntleyChristopher J Mungall
Aug 26, 2014·Journal of the American Medical Informatics Association : JAMIA·Sameer PradhanGuergana Savova
Aug 22, 2015·Yearbook of Medical Informatics·M Da SilveiraC Pruski
Mar 31, 2016·Journal of the American Medical Informatics Association : JAMIA·John D OsborneGeoff Gordon

❮ Previous
Next ❯

Citations

Dec 16, 2020·Journal of the American Medical Informatics Association : JAMIA·Denis Newman-GriffisEric Fosler-Lussier
Jun 22, 2021·Journal of the American Medical Informatics Association : JAMIA·Eunsuk Chang, Javed Mostafa

❮ Previous
Next ❯

Software Mentioned

SNOMED
UMLS
BRAT
SEMEVAL20
SNOMED CT
SEMEVAL2015
ShareClef
CUILESS2016
CT
GALEN

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.

Related Papers

Journal of the American Medical Informatics Association : JAMIA
Rohit J Kate
BMC Bioinformatics
Michael BadaLawrence E Hunter
Studies in Health Technology and Informatics
Jean-Baptiste LamyCatherine Duclos
Journal of the American Medical Informatics Association : JAMIA
Sameer PradhanGuergana Savova
© 2022 Meta ULC. All rights reserved