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A French clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated Text corpus (MERLOT) [<Journal>]
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DNB Subject Category Language
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A French clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated Text corpus (MERLOT)
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In: ISSN: 1574-020X ; EISSN: 1574-0218 ; Language Resources and Evaluation ; https://hal.archives-ouvertes.fr/hal-01631743 ; Language Resources and Evaluation, Springer Verlag, 2017, 52 (2), pp.571-601. ⟨10.1007/s10579-017-9382-y⟩ (2017)
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Annotation Guidelines BIONLP-ST 2016 SeeDev task
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In: https://hal.inrae.fr/hal-02795594 ; 2016, pp.47 ; https://sites.google.com/site/bionlpst2016/tasks/seedev/AnnotationGuidelinesBIONLP-ST2016-SeeDevtask%285%29.pdf (2016)
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Shared Task SeeDev : Extraction de régulations impliquées dans le développement de la graine d’Arabidopsis thaliana à partir de publications scientifiques
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In: Les journées Bioinformatique de l'Inra ; https://hal.archives-ouvertes.fr/hal-01455855 ; Les journées Bioinformatique de l'Inra, Mar 2016, Montpellier, France. pp.1 (2016)
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Overview of the regulatory network of plant seed development (SeeDev) task at the BioNLP shared task 2016
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In: Proceedings of the 4th BioNLP Shared Task Workshop ; BioNLP Shared Task ; https://hal.archives-ouvertes.fr/hal-01455854 ; BioNLP Shared Task, Aug 2016, Berlin, Germany. pp.113 ; https://www.aclweb.org/anthology/W/W16/W16-3001.pdf (2016)
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OntoBiotope, technologies sémantiques pour l’étude des habitats microbiens
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In: Méta-omiques des Ecosystèmes Microbiens ; https://hal.inrae.fr/hal-02889012 ; Méta-omiques des Ecosystèmes Microbiens, Sep 2015, Paris, France (2015)
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Information extraction from articles for the elaboration of the regulatory networks involved in Arabidopsis seed development
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In: 26th International Conference on Arabidopsis Research ; https://hal.archives-ouvertes.fr/hal-01524850 ; 26th International Conference on Arabidopsis Research, Jul 2015, Paris, France (2015)
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Knowledge model of regulatory networks involved in Arabidopsis seed development for information extraction and integration from text
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Chaix, Estelle; Dubreucq, Bertrand; Valsamou, Dialekti; Fatihi, Abdelhak; Bossy, Robert; Deleger, Louise; Zweigenbaum, Pierre; Bessieres, Philippe; Lepiniec, Loic; Nédellec, Claire
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In: BioCreative 5 ; https://hal.archives-ouvertes.fr/hal-01512197 ; BioCreative 5, Sep 2015, Madrid, Spain (2015)
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Abstract:
A comprehensive understanding of the molecular network underlying seed development regulations remains a major scientific challenge with important potential impact for fundamental research, agriculture and industry. Seed development requires the coordinated growth of different tissues that involves complex genetics and environmental regulations. Most of this knowledge is spread in thousands of articles. Integrating knowledge conveyed by text with knowledge derived from experimental data requires a common model in view of modeling in systems biology. In this work, we focused on a model organism, Arabidopsis thaliana. We designed a knowledge model that meet the needs of text-mining, (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse to other plant systems. The model defines 6 sets of entity types that cover 16 types of biological entities and external factors. The first two sets are central in regulation description: genetic process entities and their products, such as molecular entities or biochemical processes. The last four, Genotypes, Tissues, Development phase and Environmental factor, define the observed conditions for the regulation. Events represent binary and n-ary relations between entities: three event types describe regulations involving gene expression, metabolic pathways, regulatory networks and molecular accumulation, which is critical in seed development. Additional qualifiers specify involvement, activation, inhibition or requirement. Molecular interactions are represented by three biological events: Binds_to, Encodes and Interacts_with. Comparison, Belongs_To, Found_In and Found_During events are used to describe similarity, membership, spatial and temporal relations among entities. All events have Negation and Speculation modalities. This model was used by biology experts to manually annotate a reference corpus and train our Alvis methods that have shown its relevance.
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Keyword:
[INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]; [SDV.BV]Life Sciences [q-bio]/Vegetal Biology; développement de la graine; extraction d'information; text-mining
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URL: https://hal.archives-ouvertes.fr/hal-01512197/file/Biocreative2015_knowledge_model_Arabidopsis_ECVfinaleV4_1.pdf https://hal.archives-ouvertes.fr/hal-01512197 https://hal.archives-ouvertes.fr/hal-01512197/document
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Information extraction from articles for the elaboration of the regulatory networks involved in Arabidopsis seed development ...
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Information Extraction Challenge Gene Regulation Network in Arabidopsis thaliana (GRNA) ...
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Automatic computation of CHA2DS2-VASc score: information extraction from clinical texts for thromboembolism risk assessment.
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In: AMIA . Annual Symposium proceedings [electronic resource] / AMIA Symposium. AMIA Symposium. ; https://hal.archives-ouvertes.fr/hal-00748588 ; AMIA . Annual Symposium proceedings [electronic resource] / AMIA Symposium. AMIA Symposium., 2011, 2011, pp.501-10 (2011)
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Automatic computation of CHA2DS2-VASc score: Information extraction from clinical texts for thromboembolism risk assessment
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Named and specific entity detection in varied data: the Quaero named entity baseline evaluation
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In: 7. Conference on international language resources and evaluation ; https://hal.inrae.fr/hal-02754184 ; 7. Conference on international language resources and evaluation, May 2010, Valletta, Malta ; http://www.lrec-conf.org/proceedings/lrec2010/index.html (2010)
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Named and specific entity detection in varied data: The Quaero Named Entity baseline evaluation
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In: Seventh International Language Resources and Evaluation (LREC'10) ; https://hal.archives-ouvertes.fr/hal-02496836 ; Seventh International Language Resources and Evaluation (LREC'10), 2010, La Valette, Malta (2010)
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Morphosemantic parsing of medical compound words: Transferring a French analyzer to English
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In: ISSN: 1386-5056 ; International Journal of Medical Informatics ; https://hal.archives-ouvertes.fr/hal-00413362 ; International Journal of Medical Informatics, Elsevier, 2009, 78 (1), pp.48-55 (2009)
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Paraphrase Acquisition from Comparable Medical Corpora of Specialized and Lay Texts
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Analyse morphosémantique des composés savants : transposition du français à l'anglais
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In: TALN ; https://halshs.archives-ouvertes.fr/halshs-00157869 ; TALN, Jun 2007, Toulouse, France. pp.79-88 (2007)
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Defining Medical Words : Transposing Morphosemantic Analysis from French to English
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In: Proceedings of the 12th Medinfo Conference ; 12th International Conference MEDINFO ; https://halshs.archives-ouvertes.fr/halshs-00157857 ; 12th International Conference MEDINFO, Aug 2007, Brisbane, Australia. pp.535-539 (2007)
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