SIA: A Scalable Interoperable Annotation Server for Biomedical Named Entities

April 08, 2020 · Entered Twilight · 🏛 Journal of Cheminformatics

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Authors Johannes Kirschnick, Philippe Thomas, Roland Roller, Leonhard Hennig arXiv ID 2004.03822 Category cs.CL: Computation & Language Cross-listed cs.IR Citations 1 Venue Journal of Cheminformatics Repository https://github.com/Erechtheus/sia ⭐ 3 Last Checked 2 months ago

Abstract

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.