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SIFR Annotator: Ontology-Based Semantic Annotation of French Biomedical Text and Clinical Notes
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In: ISSN: 1471-2105 ; BMC Bioinformatics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01934127 ; BMC Bioinformatics, BioMed Central, 2018, 19 (1), pp.405-431. ⟨10.1186/s12859-018-2429-2⟩ (2018)
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Abstract:
International audience ; Background: Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as domain terminologies or ontologies are only available in English, and cannot be readily applied to other languages, due to fundamental linguistic differences. However, semantic resources are required to design semantic indexes and transform biomedical (text)data into knowledge for better information mining and retrieval. Results: We present the SIFR Annotator (http://bioportal.lirmm.fr/annotator), a publicly accessible ontology-based annotation web service to process biomedical text data in French. The service, developed during the Semantic Indexing of French Biomedical Data Resources (2013-2019) project is included in the SIFR BioPortal, an open platform to host French biomedical ontologies and terminologies based on the technology developed by the US National Center for Biomedical Ontology. The portal facilitates use and fostering of ontologies by offering a set of services-search, mappings, metadata, versioning, visualization, recommendation-including for annotation purposes. We introduce the adaptations and improvements made in applying the technology to French as well as a number of language independent additional features-implemented by means of a proxy architecture-in particular annotation scoring and clinical context detection. We evaluate the performance of the SIFR Annotator on different biomedical data, using available French corpora-Quaero (titles from French MEDLINE abstracts and EMEA drug labels) and CépiDC (ICD-10 coding of death certificates)-and discuss our results with respect to the CLEF eHealth information extraction tasks. Conclusions: We show the web service performs comparably to other knowledge-based annotation approaches in recognizing entities in biomedical text and reach state-of-the-art levels in clinical context detection (negation, experiencer, temporality). Additionally, the SIFR Annotator is the first openly web accessible tool to annotate and contextualize French biomedical text with ontology concepts leveraging a dictionary currently made of 28 terminologies and ontologies and 333 K concepts. The code is openly available, and we also provide a Docker packaging for easy local deployment to process sensitive (e.g., clinical) data in-house (https://github.com/sifrproject).
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Keyword:
[INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing; [INFO.INFO-WB]Computer Science [cs]/Web; Biomedical ontologies; NCBO BioPortal; Semantic annotation; Semantic indexing; SIFR Annotator; SIFR BioPortal
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URL: https://doi.org/10.1186/s12859-018-2429-2
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01934127
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01934127/document
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01934127/file/s12859-018-2429-2.pdf
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Challenges for ontology repositories and applications to biomedicine & agronomy
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In: 4th Annual International Symposium on Information Management and Big Data ; SIMBig: Symposium on Information Management and Big Data ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01679500 ; SIMBig: Symposium on Information Management and Big Data, Sep 2017, Lima, Peru. pp.25-37 ; http://simbig.org/SIMBig2017/ (2017)
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Réconciliation d'alignements multilingues dans BioPortal
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In: 27es Journées francophones d'Ingénierie des Connaissances ; IC: Ingénierie des Connaissances ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01395900 ; IC: Ingénierie des Connaissances, Jun 2016, Montpellier, France ; https://ic2016.sciencesconf.org/ (2016)
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Multilingual Mapping Reconciliation between English-French Biomedical Ontologies
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In: 6th International Conference on Web Intelligence, Mining and Semantics ; WIMS: Web Intelligence, Mining and Semantics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01395880 ; WIMS: Web Intelligence, Mining and Semantics, Jun 2016, Nîmes, France. ⟨10.1145/2912845.2912847⟩ ; http://wims2016.mines-ales.fr/ (2016)
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Roadmap for a multilingual BioPortal
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In: 4th Workshop on the Multilingual Semantic Web ; MSW: Multilingual Semantic Web ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01172218 ; MSW: Multilingual Semantic Web, Jun 2015, Portoroz, Slovenia (2015)
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Scoring semantic annotations returned by the NCBO Annotator
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In: 7th International Semantic Web Applications and Tools for Life Sciences ; SWAT4LS: Semantic Web Applications and Tools for Life Sciences ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01099860 ; SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2014, Berlin, Germany ; http://ceur-ws.org/Vol-1320/ (2014)
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The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
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In: American Medical Informatics Association Annual Symposium, AMIA'10 ; https://hal.archives-ouvertes.fr/hal-00558033 ; American Medical Informatics Association Annual Symposium, AMIA'10, Nov 2010, Washington, DC, United States. pp.6 (2010)
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What Four Million Mappings Can Tell You about Two Hundred Ontologies
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In: 8th International Semantic Web Conference, ISWC'09 ; https://hal.archives-ouvertes.fr/hal-00489094 ; 8th International Semantic Web Conference, ISWC'09, Oct 2009, Washington DC, United States. pp.229-242 (2009)
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