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 …

Community challenges in biomedical text mining over 10 years: success, failure and the future

CC Huang, Z Lu - Briefings in bioinformatics, 2016 - academic.oup.com
One effective way to improve the state of the art is through competitions. Following the
success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics …

Domain-specific language model pretraining for biomedical natural language processing

Y Gu, R Tinn, H Cheng, M Lucas, N Usuyama… - ACM Transactions on …, 2021 - dl.acm.org
Pretraining large neural language models, such as BERT, has led to impressive gains on
many natural language processing (NLP) tasks. However, most pretraining efforts focus on …

The role of ontologies in biological and biomedical research: a functional perspective

R Hoehndorf, PN Schofield… - Briefings in …, 2015 - academic.oup.com
Ontologies are widely used in biological and biomedical research. Their success lies in their
combination of four main features present in almost all ontologies: provision of standard …

GNormPlus: an integrative approach for tagging genes, gene families, and protein domains

CH Wei, HY Kao, Z Lu - BioMed research international, 2015 - Wiley Online Library
The automatic recognition of gene names and their associated database identifiers from
biomedical text has been widely studied in recent years, as these tasks play an important …

Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort

JI Feinberg, KM Bakulski, AE Jaffe… - International journal …, 2015 - academic.oup.com
Background: Epigenetic mechanisms such as altered DNA methylation have been
suggested to play a role in autism, beginning with the classical association of Prader-Willi …

Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort

JI Feinberg, R Schrott, C Ladd-Acosta… - Molecular …, 2024 - nature.com
There is a need to consider paternal contributions to autism spectrum disorder (ASD) more
strongly. Autism etiology is complex, and heritability is not explained by genetics alone …

Semantic annotation in biomedicine: the current landscape

J Jovanović, E Bagheri - Journal of biomedical semantics, 2017 - Springer
The abundance and unstructured nature of biomedical texts, be it clinical or research
content, impose significant challenges for the effective and efficient use of information and …

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank

Y Mao, Z Lu - Journal of biomedical semantics, 2017 - Springer
Background MeSH indexing is the task of assigning relevant MeSH terms based on a
manual reading of scholarly publications by human indexers. The task is highly important for …

[HTML][HTML] A fine-tuned bidirectional encoder representations from transformers model for food named-entity recognition: Algorithm development and validation

R Stojanov, G Popovski, G Cenikj… - Journal of Medical …, 2021 - jmir.org
Background Recently, food science has been garnering a lot of attention. There are many
open research questions on food interactions, as one of the main environmental factors, with …