SIA: A Scalable Interoperable Annotation Server for Biomedical Named Entities
This work addresses the cumbersome integration of biomedical annotation tools for researchers, though it appears incremental as it builds on existing tools and tasks.
The authors tackled the problem of integrating biomedical text mining tools into customized workflows by developing SIA, a scalable and interoperable annotation server that covers six named entity types and is freely available under an open-source license.
Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., Chemicals, Diseases, Genes, miRNA, Mutations, and Organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia.