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. 2018 Dec 14;10(1):63.
doi: 10.1186/s13321-018-0319-2.

SIA: a scalable interoperable annotation server for biomedical named entities

Johannes Kirschnick  1 , Philippe Thomas  1 , Roland Roller  1 , Leonhard Hennig  2
Affiliations

SIA: a scalable interoperable annotation server for biomedical named entities

Johannes Kirschnick et al. J Cheminform. .

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 .

Keywords: Annotation service; Extensibility; Robustness; Scalability; Text mining.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
General architecture of SIA. The front end handles new requests and forwards them to the back end over a message bus. Each message is transformed through a series of components, which in turn are connected via named queues. The result handler collects the annotation responses and returns them to the calling client
Fig. 2
Fig. 2
Processing statistics over a four week period and request times per corpus, reporting complete processing and annotation timings separately
See this image and copyright information in PMC

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