WorldCat Identities

Abdaoui, Amine

Overview
Works: 3 works in 3 publications in 1 language and 5 library holdings
Roles: Author
Publication Timeline
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Most widely held works by Amine Abdaoui
FEEL: a French Expanded Emotion Lexicon by Amine Abdaoui( )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes by Andon Tchechmedjiev( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

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

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

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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Audience level: 0.95 (from 0.88 for Enhanced f ... to 0.97 for SIFR annot ...)

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