SIA: a scalable interoperable annotation server for biomedical named entities

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 custo...

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Detalles Bibliográficos
Autores principales: Kirschnick, Johannes, Thomas, Philippe, Roller, Roland, Hennig, Leonhard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755617/
https://www.ncbi.nlm.nih.gov/pubmed/30552534
http://dx.doi.org/10.1186/s13321-018-0319-2
Descripción
Sumario: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.

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