Recent developments in clinical terminologies—SNOMED CT, LOINC, and RxNorm

O Bodenreider, R Cornet… - Yearbook of medical …, 2018 - thieme-connect.com
Objective: To discuss recent developments in clinical terminologies. SNOMED CT
(Systematized Nomenclature of Medicine Clinical Terms) is the world's largest clinical …

[HTML][HTML] Assessing the practice of biomedical ontology evaluation: Gaps and opportunities

M Amith, Z He, J Bian, JA Lossio-Ventura… - Journal of biomedical …, 2018 - Elsevier
With the proliferation of heterogeneous health care data in the last three decades,
biomedical ontologies and controlled biomedical terminologies play a more and more …

K-bert: Enabling language representation with knowledge graph

W Liu, P Zhou, Z Zhao, Z Wang, Q Ju, H Deng… - Proceedings of the …, 2020 - ojs.aaai.org
Pre-trained language representation models, such as BERT, capture a general language
representation from large-scale corpora, but lack domain-specific knowledge. When reading …

Named entity recognition and normalization applied to large-scale information extraction from the materials science literature

L Weston, V Tshitoyan, J Dagdelen… - Journal of chemical …, 2019 - ACS Publications
The number of published materials science articles has increased manyfold over the past
few decades. Now, a major bottleneck in the materials discovery pipeline arises in …

Representation of rare diseases in health information systems: the Orphanet approach to serve a wide range of end users

A Rath, A Olry, F Dhombres, MM Brandt… - Human …, 2012 - Wiley Online Library
Rare disorders are scarcely represented in international classifications and therefore
invisible in information systems. One of the major needs in health information systems and …

Ontological realism: A methodology for coordinated evolution of scientific ontologies

B Smith, W Ceusters - Applied ontology, 2010 - content.iospress.com
Since 2002 we have been testing and refining a methodology for ontology development that
is now being used by multiple groups of researchers in different life science domains. Gary …

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction

FZ Smaili, X Gao, R Hoehndorf - Bioinformatics, 2019 - academic.oup.com
Motivation Ontologies are widely used in biology for data annotation, integration and
analysis. In addition to formally structured axioms, ontologies contain meta-data in the form …

Concept annotation in the CRAFT corpus

M Bada, M Eckert, D Evans, K Garcia, K Shipley… - BMC …, 2012 - Springer
Background Manually annotated corpora are critical for the training and evaluation of
automated methods to identify concepts in biomedical text. Results This paper presents the …

Onto2vec: joint vector-based representation of biological entities and their ontology-based annotations

FZ Smaili, X Gao, R Hoehndorf - Bioinformatics, 2018 - academic.oup.com
Motivation Biological knowledge is widely represented in the form of ontology-based
annotations: ontologies describe the phenomena assumed to exist within a domain, and the …

Past and future uses of text mining in ecology and evolution

MJ Farrell, L Brierley, A Willoughby… - Proceedings of the …, 2022 - royalsocietypublishing.org
Ecology and evolutionary biology, like other scientific fields, are experiencing an
exponential growth of academic manuscripts. As domain knowledge accumulates, scientists …