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. 2018 Jun 1;34(11):1962-1965.
doi: 10.1093/bioinformatics/bty009.

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator

Andon Tchechmedjiev  1 , Amine Abdaoui  1 , Vincent Emonet  1 , Soumia Melzi  1 , Jitendra Jonnagaddala  2 , Clement Jonquet  1   3
Affiliations

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator

Andon Tchechmedjiev et al. Bioinformatics. .

Abstract

Summary: Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014).

Availability and implementation: The Annotator+ has been successfully integrated into the SIFR BioPortal platform-an implementation of NCBO BioPortal for French biomedical terminologies and ontologies-to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject).

Contact: andon.tchechmedjiev@lirmm.fr.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
User Interface of the NCBO Annotator+ Web service (http://bioportal.lirmm.fr/ncbo_annotatorplus) illustrating new features. To reproduce this example with the Web service, use the URL: https://goo.gl/BTrNzJ
Fig. 2.
Fig. 2.
Annotation results for the example sentence from Figure 1
Fig. 3.
Fig. 3.
NCBO Annotator+ proxy-like Web service architecture
See this image and copyright information in PMC

References

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