BioRED: a rich biomedical relation extraction dataset

L Luo, PT Lai, CH Wei, CN Arighi… - Briefings in …, 2022 - academic.oup.com
Automated relation extraction (RE) from biomedical literature is critical for many downstream
text mining applications in both research and real-world settings. However, most existing …

Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives

J Xu, P Yang, S Xue, B Sharma, M Sanchez-Martin… - Human genetics, 2019 - Springer
In the field of cancer genomics, the broad availability of genetic information offered by next-
generation sequencing technologies and rapid growth in biomedical publication has led to …

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 …

A neural named entity recognition and multi-type normalization tool for biomedical text mining

D Kim, J Lee, CH So, H Jeon, M Jeong, Y Choi… - IEEE …, 2019 - ieeexplore.ieee.org
The amount of biomedical literature is vast and growing quickly, and accurate text mining
techniques could help researchers to efficiently extract useful information from the literature …

Getting more out of biomedical documents with GATE's full lifecycle open source text analytics

H Cunningham, V Tablan, A Roberts… - PLoS computational …, 2013 - journals.plos.org
This software article describes the GATE family of open source text analysis tools and
processes. GATE is one of the most widely used systems of its type with yearly download …

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC

A Allot, Y Peng, CH Wei, K Lee, L Phan… - Nucleic acids …, 2018 - academic.oup.com
The identification and interpretation of genomic variants play a key role in the diagnosis of
genetic diseases and related research. These tasks increasingly rely on accessing relevant …

tmVar: a text mining approach for extracting sequence variants in biomedical literature

CH Wei, BR Harris, HY Kao, Z Lu - Bioinformatics, 2013 - academic.oup.com
Motivation: Text-mining mutation information from the literature becomes a critical part of the
bioinformatics approach for the analysis and interpretation of sequence variations in …

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

M Krallinger, A Valencia, L Hirschman - Genome biology, 2008 - Springer
Efficient access to information contained in online scientific literature collections is essential
for life science research, playing a crucial role from the initial stage of experiment planning …

Text mining genotype-phenotype relationships from biomedical literature for database curation and precision medicine

A Singhal, M Simmons, Z Lu - PLoS computational biology, 2016 - journals.plos.org
The practice of precision medicine will ultimately require databases of genes and mutations
for healthcare providers to reference in order to understand the clinical implications of each …

Towards precision medicine: advances in computational approaches for the analysis of human variants

TA Peterson, E Doughty, MG Kann - Journal of molecular biology, 2013 - Elsevier
Variations and similarities in our individual genomes are part of our history, our heritage,
and our identity. Some human genomic variants are associated with common traits such as …