MOTIVATION: Significant effort has been spent by curators to create coding 
systems for phenotypes such as the Human Phenotype Ontology, as well as 
disease-phenotype annotations. We aim to support the discovery of 
literature-based phenotypes and integrate them into the knowledge discovery 
process.
RESULTS: PheneBank is a Web-portal for retrieving human phenotype-disease 
associations that have been text-mined from the whole of Medline. Our approach 
exploits state-of-the-art machine learning for concept identification by 
utilizing an expert annotated rare disease corpus from the PMC Text Mining 
subset. Evaluation of the system for entities is conducted on a gold-standard 
corpus of rare disease sentences and for associations against the Monarch 
initiative data.
AVAILABILITY AND IMPLEMENTATION: The PheneBank Web-portal freely available at 
http://www.phenebank.org. Annotated Medline data is available from Zenodo at 
DOI: 10.5281/zenodo.1408800. Semantic annotation software is freely available 
for non-commercial use at GitHub: https://github.com/pilehvar/phenebank.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.