Beyond accuracy: creating interoperable and scalable text-mining web services

Bioinformatics. 2016 Jun 15;32(12):1907-10. doi: 10.1093/bioinformatics/btv760. Epub 2016 Feb 16.


The biomedical literature is a knowledge-rich resource and an important foundation for future research. With over 24 million articles in PubMed and an increasing growth rate, research in automated text processing is becoming increasingly important. We report here our recently developed web-based text mining services for biomedical concept recognition and normalization. Unlike most text-mining software tools, our web services integrate several state-of-the-art entity tagging systems (DNorm, GNormPlus, SR4GN, tmChem and tmVar) and offer a batch-processing mode able to process arbitrary text input (e.g. scholarly publications, patents and medical records) in multiple formats (e.g. BioC). We support multiple standards to make our service interoperable and allow simpler integration with other text-processing pipelines. To maximize scalability, we have preprocessed all PubMed articles, and use a computer cluster for processing large requests of arbitrary text.

Availability and implementation: Our text-mining web service is freely available at

Contact: :

MeSH terms

  • Data Mining*
  • Humans
  • Internet*
  • PubMed*
  • Software*