bioNerDS: exploring bioinformatics' database and software use through literature mining
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 …
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
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 …
However, while there is an ever expanding choice of bioinformatics resources to use …
Ambiguity and variability of database and software names in bioinformatics
Background There are numerous options available to achieve various tasks in
bioinformatics, but until recently, there were no tools that could systematically identify …
bioinformatics, but until recently, there were no tools that could systematically identify …
A machine learning-enabled open biodata resource inventory from the scientific literature
Modern biological research depends on data resources. These resources archive difficult-to-
reproduce data and provide added-value aggregation, curation, and analyses. Collectively …
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
With the proliferation of genomic sequence data for biomedical research, the exploration of
human genetic information by domain experts requires a comprehensive interrogation 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 …
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
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 …
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
High-throughput experiments and bioinformatics techniques are creating an exploding
volume of data that are becoming overwhelming to keep track of for biologists and …
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
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 …
attention. Even though there are several attempts to understand the field of bioinformatics by …
Quantitative assessment of dictionary-based protein named entity tagging
Objective: Natural language processing (NLP) approaches have been explored to manage
and mine information recorded in biological literature. A critical step for biological literature …
and mine information recorded in biological literature. A critical step for biological literature …