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 …

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 …

Tools and data services registry: a community effort to document bioinformatics resources

J Ison, K Rapacki, H Ménager, M Kalaš… - Nucleic acids …, 2016 - academic.oup.com
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to
improvement in human health, agriculture and the environment. In support of these …

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 …

BioDEAL: community generation of biological annotations

P Breimyer, N Green, V Kumar… - BMC Medical Informatics …, 2009 - Springer
Background Publication databases in biomedicine (eg, PubMed, MEDLINE) are growing
rapidly in size every year, as are public databases of experimental biological data and …

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 …

Integration of open access literature into the RCSB Protein Data Bank using BioLit

A Prlić, MA Martinez, D Dimitropoulos, B Beran… - BMC …, 2010 - Springer
Background Biological data have traditionally been stored and made publicly available
through a variety of on-line databases, whereas biological knowledge has traditionally been …

Utopia documents: linking scholarly literature with research data

TK Attwood, DB Kell, P McDermott, J Marsh… - …, 2010 - academic.oup.com
Motivation: In recent years, the gulf between the mass of accumulating-research data and
the massive literature describing and analyzing those data has widened. The need for …

[PDF][PDF] Building the scientific knowledge mine (SciKnowMine): A community-driven framework for text mining tools in direct service to biocuration

C Ramakrishnan, WA Baumgartner Jr… - New Challenges For …, 2010 - academia.edu
Although there exist many high-performing text-mining tools to address literature biocuration
(populating biomedical databases from the published literature), the challenge of delivering …

Automatic categorization of diverse experimental information in the bioscience literature

R Fang, G Schindelman, KV Auken, J Fernandes… - BMC …, 2012 - Springer
Background Curation of information from bioscience literature into biological knowledge
databases is a crucial way of capturing experimental information in a computable form …