bioNerDS: exploring bioinformatics' database and software use through literature mining

G Duck, G Nenadic, A Brass, DL Robertson… - BMC …, 2013 - Springer
Background Biology-focused databases and software define bioinformatics and their use is
central to computational biology. In such a complex and dynamic field, it is of interest to …

A survey of bioinformatics database and software usage through mining the literature

G Duck, G Nenadic, M Filannino, A Brass… - PloS one, 2016 - journals.plos.org
Computer-based resources are central to much, if not most, biological and medical research.
However, while there is an ever expanding choice of bioinformatics resources to use …

Ambiguity and variability of database and software names in bioinformatics

G Duck, A Kovacevic, DL Robertson, R Stevens… - Journal of biomedical …, 2015 - Springer
Background There are numerous options available to achieve various tasks in
bioinformatics, but until recently, there were no tools that could systematically identify …

A machine learning-enabled open biodata resource inventory from the scientific literature

HJ Imker, KE Schackart III, AM Istrate, CE Cook - Plos one, 2023 - journals.plos.org
Modern biological research depends on data resources. These resources archive difficult-to-
reproduce data and provide added-value aggregation, curation, and analyses. Collectively …

pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature

PH Li, TF Chen, JY Yu, SH Shih, CH Su… - Nucleic Acids …, 2022 - academic.oup.com
With the proliferation of genomic sequence data for biomedical research, the exploration of
human genetic information by domain experts requires a comprehensive interrogation of …

[HTML][HTML] SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

A Venkatesan, JH Kim, F Talo, M Ide-Smith… - Wellcome open …, 2016 - ncbi.nlm.nih.gov
The tremendous growth in biological data has resulted in an increase in the number of
research papers being published. This presents a great challenge for scientists in searching …

BioLitMine: advanced mining of biomedical and biological literature about human genes and genes from major model organisms

Y Hu, V Chung, A Comjean, J Rodiger… - G3: Genes …, 2020 - academic.oup.com
The accumulation of biological and biomedical literature outpaces the ability of most
researchers and clinicians to stay abreast of their own immediate fields, let alone a broader …

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

A Névéol, WJ Wilbur, Z Lu - Database, 2012 - academic.oup.com
High-throughput experiments and bioinformatics techniques are creating an exploding
volume of data that are becoming overwhelming to keep track of for biologists and …

Detecting the knowledge structure of bioinformatics by mining full-text collections

M Song, SY Kim - Scientometrics, 2013 - Springer
Bioinformatics is a fast-growing, diverse research field that has recently gained much public
attention. Even though there are several attempts to understand the field of bioinformatics by …

Quantitative assessment of dictionary-based protein named entity tagging

H Liu, ZZ Hu, M Torii, C Wu… - Journal of the American …, 2006 - academic.oup.com
Objective: Natural language processing (NLP) approaches have been explored to manage
and mine information recorded in biological literature. A critical step for biological literature …