Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison

B Song, F Li, Y Liu, X Zeng - Briefings in Bioinformatics, 2021 - academic.oup.com
The biomedical literature is growing rapidly, and the extraction of meaningful information
from the large amount of literature is increasingly important. Biomedical named entity …

Information retrieval and text mining technologies for chemistry

M Krallinger, O Rabal, A Lourenco, J Oyarzabal… - Chemical …, 2017 - ACS Publications
Efficient access to chemical information contained in scientific literature, patents, technical
reports, or the web is a pressing need shared by researchers and patent attorneys from …

Quantifying the advantage of domain-specific pre-training on named entity recognition tasks in materials science

A Trewartha, N Walker, H Huo, S Lee, K Cruse… - Patterns, 2022 - cell.com
A bottleneck in efficiently connecting new materials discoveries to established literature has
arisen due to an increase in publications. This problem may be addressed by using named …

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

R Leaman, Z Lu - Bioinformatics, 2016 - academic.oup.com
Motivation: Text mining is increasingly used to manage the accelerating pace of the
biomedical literature. Many text mining applications depend on accurate named entity …

[HTML][HTML] Opportunities and challenges of text mining in materials research

O Kononova, T He, H Huo, A Trewartha, EA Olivetti… - Iscience, 2021 - cell.com
Research publications are the major repository of scientific knowledge. However, their
unstructured and highly heterogenous format creates a significant obstacle to large-scale …

The CHEMDNER corpus of chemicals and drugs and its annotation principles

M Krallinger, O Rabal, F Leitner, M Vazquez… - Journal of …, 2015 - Springer
The automatic extraction of chemical information from text requires the recognition of
chemical entity mentions as one of its key steps. When develo** supervised named entity …

[HTML][HTML] Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports

H Gurulingappa, AM Rajput, A Roberts, J Fluck… - Journal of biomedical …, 2012 - Elsevier
A significant amount of information about drug-related safety issues such as adverse effects
are published in medical case reports that can only be explored by human readers due to …

tmChem: a high performance approach for chemical named entity recognition and normalization

R Leaman, CH Wei, Z Lu - Journal of cheminformatics, 2015 - Springer
Chemical compounds and drugs are an important class of entities in biomedical research
with great potential in a wide range of applications, including clinical medicine. Locating …

HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition

L Weber, M Sänger, J Münchmeyer, M Habibi… - …, 2021 - academic.oup.com
Named entity recognition (NER) is an important step in biomedical information extraction
pipelines. Tools for NER should be easy to use, cover multiple entity types, be highly …

ChemSpot: a hybrid system for chemical named entity recognition

T Rocktäschel, M Weidlich, U Leser - Bioinformatics, 2012 - academic.oup.com
Motivation: The accurate identification of chemicals in text is important for many applications,
including computer-assisted reconstruction of metabolic networks or retrieval of information …