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Adrien Coulet

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Publications

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Discovering alignment relations with Graph Convolutional Networks: A biomedical case study

Pierre Monnin , Chedy Raïssi , Amedeo Napoli , Adrien Coulet
Semantic Web – Interoperability, Usability, Applicability, 2022, pp.1-20. ⟨10.3233/SW-210452⟩
Journal articles hal-03452182v1

Technical, Ethical, Legal, and Societal Challenges With Digital Twin Systems for the Management of Chronic Diseases in Children and Young People

David Drummond , Adrien Coulet
Journal of Medical Internet Research, 2022, 24 (10), pp.e39698. ⟨10.2196/39698⟩
Journal articles hal-03835708v1
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Projet ANR (2016-2021) « PractiKPharma » : extraction, comparaison et découverte de connaissances en pharmacogénomique

Pierre Monnin , Adrien Coulet
1024 : Bulletin de la Société Informatique de France, 2022, 19, pp.109 - 120. ⟨10.48556/sif.1024.19.109⟩
Journal articles hal-03669026v1
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Étudier les mécanismes des effets indésirables des médicaments avec l'IA explicable : expériences avec la fouille de graphes de connaissances

Pierre Monnin , Adrien Coulet
Bulletin de l'Association Française pour l'Intelligence Artificielle, 2022
Journal articles hal-03669065v1

Syntax-based transfer learning for the task of biomedical relation extraction

Joël Legrand , Yannick Toussaint , Chedy Raïssi , Adrien Coulet
Journal of Biomedical Semantics, 2021, 12 (1), ⟨10.1186/s13326-021-00248-y⟩
Journal articles hal-03330823v1
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L'équipe-projet HeKA

Adrien Coulet , Stéphanie Allassonniere , François Angoulvant , Anita Burgun , Xiaoyi Chen et al.
Bulletin de l'Association Française pour l'Intelligence Artificielle, 2021, pp.29-32
Journal articles hal-03485904v1
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Investigating ADR mechanisms with Explainable AI: a feasibility study with knowledge graph mining

Emmanuel Bresso , Pierre Monnin , Cédric Bousquet , François-Elie Calvier , Ndeye-Coumba Ndiaye et al.
BMC Medical Informatics and Decision Making, 2021, 21 (1), pp.171. ⟨10.1186/s12911-021-01518-6⟩
Journal articles hal-03240476v1

L'équipe-projet HeKA

Adrien Coulet , Stéphanie Allassonnière , François Angoulvant , Anita Burgun , Xiaoyi Chen et al.
Bulletin de l'Association Française pour l'Intelligence Artificielle, 2021, 112
Journal articles hal-03849196v1

PGxCorpus, a manually annotated corpus for pharmacogenomics

Joël Legrand , Romain Gogdemir , Cedric Bousquet , Kevin Dalleau , Marie-Dominique Devignes et al.
Scientific Data , 2020, 7, pp.3. ⟨10.1038/s41597-019-0342-9⟩
Journal articles hal-02547607v1
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PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison

Pierre Monnin , Joël Legrand , Graziella Husson , Patrice Ringot , Andon Tchechmedjiev et al.
BMC Bioinformatics, 2019, 20 (S4), ⟨10.1186/s12859-019-2693-9⟩
Journal articles hal-02103899v1

Atherosclerotic Cardiovascular Disease Risk Prediction in Disaggregated Asian and Hispanic Subgroups Using Electronic Health Records

Fatima Rodriguez , Sukyung Chung , Manuel Blum , Adrien Coulet , Sanjay Basu et al.
Journal of the American Heart Association, 2019, 8 (14), ⟨10.1161/JAHA.118.011874⟩
Journal articles hal-02196129v1
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Predicting the need for a reduced drug dose, at first prescription

Adrien Coulet , Nigam H. Shah , Maxime Wack , Mohammad Chawki , Nicolas Jay et al.
Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-018-33980-0⟩
Journal articles hal-01901566v1
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Discovering associations between adverse drug events using pattern structures and ontologies

Gabin Personeni , Emmanuel Bresso , Marie-Dominique Devignes , Michel Dumontier , Malika Smaïl-Tabbone et al.
Journal of Biomedical Semantics, 2017, 93, pp.539 - 546. ⟨10.1186/s13326-017-0137-x⟩
Journal articles hal-01576341v1
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Learning from biomedical linked data to suggest valid pharmacogenes

Kevin Dalleau , Yassine Marzougui , Sébastien da Silva , Patrice Ringot , Ndeye Coumba Ndiaye et al.
Journal of Biomedical Semantics, 2017, 8 (1), pp.16. ⟨10.1186/s13326-017-0125-1⟩
Journal articles hal-01511773v1
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Mining Electronic Health Records to Validate Knowledge in Pharmacogenomics

Adrien Coulet , Malika Smaïl-Tabbone
ERCIM News, 2016, ERCIM News 104, Special theme: Tackling Big Data in the Life Sciences, 104, pp.56
Journal articles hal-01369501v1

Using ontology-based annotation to profile disease research

Yi Liu , Adrien Coulet , Paea Lependu , Nigam H Shah
Journal of the American Medical Informatics Association, 2012, 19 (e1), pp.e177-e186. ⟨10.1136/amiajnl-2011-000631⟩
Journal articles hal-00752101v1

Guest Editorial: The state of the art in text mining and natural language processing for pharmacogenomics

Adrien Coulet , Kevin Bretonnel Cohen , Russ B. Altman
Journal of Biomedical Informatics, 2012, 45 (5), pp.825-826
Journal articles hal-00752106v1

Semantically enabling pharmacogenomic data for the realization of personalized medicine.

Matthias Samwald , Adrien Coulet , Iker Huerga , Robert L Powers , Joanne S Luciano et al.
Pharmacogenomics, 2012, 13 (2), pp.201-12. ⟨10.2217/pgs.11.179⟩
Journal articles hal-00752095v1
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Integration and publication of heterogeneous text-mined relationships on the Semantic Web

Adrien Coulet , Yael Garten , Michel Dumontier , Russ B Altman , Mark A. Musen et al.
Journal of Biomedical Semantics, 2011, 2 (S2), pp.S10
Journal articles hal-00585215v1
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NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

Clement Jonquet , Paea Lependu , Sean Falconer , Adrien Coulet , Natalya F. Noy et al.
Journal of Web Semantics, 2011, 9 (3), pp.316-324. ⟨10.1016/j.websem.2011.06.005⟩
Journal articles lirmm-00622155v2

Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application.

Adrien Coulet , Nigam H. Shah , Lawrence Hunter , Chitta Barral , Russ B Altman et al.
Pacific Symposium on Biocomputing, 2010, pp.485-7
Journal articles inria-00549705v1

Recent progress in automatically extracting information from the pharmacogenomic literature.

Yael Garten , Adrien Coulet , Russ B Altman
Pharmacogenomics / Personalized Medicine, 2010, 11 (10), pp.1467-89. ⟨10.2217/pgs.10.136⟩
Journal articles inria-00549699v1

Using text to build semantic networks for pharmacogenomics

Adrien Coulet , Nigam H Shah , Yael Garten , Mark A. Musen , Russ B Altman et al.
Journal of Biomedical Informatics, 2010, 43 (6), pp.1009-19. ⟨10.1016/j.jbi.2010.08.005⟩
Journal articles inria-00549695v1

Ontology-guided data preparation for discovering genotype-phenotype relationships

Adrien Coulet , Malika Smaïl-Tabbone , Pascale Benlian , Amedeo Napoli , Marie-Dominique Devignes et al.
BMC Bioinformatics, 2008, 9 (Suppl 4), pp.S3. ⟨10.1186/1471-2105-9-S4-S3⟩
Journal articles inria-00338669v1
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Matching Pharmacogenomic Knowledge: Particularities, Results, and Perspectives

Pierre Monnin , Adrien Coulet
17th International Workshop on Ontology Matching : OM-2022, Oct 2022, Virtual, China
Conference papers hal-03835712v1
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Combiner plongements de graphes et clustering pour l'alignement de connaissances pharmacogénomiques

Pierre Monnin , Chedy Raïssi , Amedeo Napoli , Adrien Coulet
Santé & IA 2022 - Journée Santé et Intelligence Artificielle (Evènement affilié à PFIA 2022), Jun 2022, Saint-Etienne, France
Conference papers hal-03754776v1
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An analogy based framework for patient-stay identification in healthcare

Safa Alsaidi , Miguel Couceiro , Esteban Marquer , Sophie Quennelle , Anita Burgun et al.
ATA@ICCBR 2022 - Workshop Analogies: from Theory to Applications, Sep 2022, Nancy, France
Conference papers hal-03763772v1
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Exploring Analogical Inference in Healthcare

Safa Alsaidi , Miguel Couceiro , Sophie Quennelle , Anita Burgun , Nicolas Garcelon et al.
IARML@IJCAI-ECAI’2022: Workshop on the Interactions between Analogical Reasoning and Machine Learning, at IJCAI-ECAI’2022, Jul 2022, Vienna, Austria
Conference papers hal-03955354v1
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Expérimentations autour des architectures d'apprentissage par transfert pour l'extraction de relations biomédicales

Walid Hafiane , Joël Legrand , Yannick Toussaint , Adrien Coulet
EGC 2021 - 21ème édition de la conférence "Extraction et Gestion des Connaissances", Jan 2021, Montpellier / Virtuel, France
Conference papers hal-03073601v1
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Using an ontological representation of chemotherapy toxicities for guiding information extraction and integration from EHRs

Alice Rogier , Adrien Coulet , Bastien Rance
Medinfo 2021 - 18th World Congress on Medical and Health Informatics, Oct 2021, Virtual conference, Australia
Conference papers hal-03364585v1
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Tackling scalability issues in mining path patterns from knowledge graphs: a preliminary study

Pierre Monnin , Emmanuel Bresso , Miguel Couceiro , Malika Smaïl-Tabbone , Amedeo Napoli et al.
ALGOS 2020 - 1st International Conference on Algebras, Graphs and Ordered Sets, Aug 2020, Nancy, France
Conference papers hal-02913224v1
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Knowledge-Based Matching of $n$-ary Tuples

Pierre Monnin , Miguel Couceiro , Amedeo Napoli , Adrien Coulet
ICCS 2020 - 25th International Conference on Conceptual Structures, Sep 2020, Bolzano / Virtual, Italy. pp.48-56, ⟨10.1007/978-3-030-57855-8_4⟩
Conference papers hal-02493067v1
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Knowledge Reconciliation with Graph Convolutional Networks: Preliminary Results

Pierre Monnin , Chedy Raïssi , Amedeo Napoli , Adrien Coulet
DL4KG2019 - Workshop on Deep Learning for Knowledge Graphs, Jun 2019, Portoroz, Slovenia
Conference papers hal-02155546v1
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Creating Fair Models of Atherosclerotic Cardiovascular Disease Risk

Stephen Pfohl , Ben Marafino , Adrien Coulet , Fatima Rodriguez , Latha Palaniappan et al.
AIES '19 - Proceedings of the 2019 AAAI/ACM Conference on AI, Ethics, and Society, Jan 2019, Honolulu, United States. pp.271-278, ⟨10.1145/3306618.3314278⟩
Conference papers hal-02388730v1
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Syntax-based Transfer Learning for the Task of Biomedical Relation Extraction

Joël Legrand , Yannick Toussaint , Chedy Raïssi , Adrien Coulet
LOUHI 2018 - The Ninth International Workshop on Health Text Mining and Information Analysis, Oct 2018, Brussels, Belgium
Conference papers hal-01869071v1
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Combining Concept Annotation and Pattern Structures for Guiding Ontology Mapping

Pierre Monnin , Amedeo Napoli , Adrien Coulet
FCA4AI@IJCAI2018 - 6th International Workshop "What can FCA do for Artificial Intelligence?", Jul 2018, Stockholm, Sweden
Conference papers hal-01858391v1
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Découverte d'associations entre Evénements Indésirables Médicamenteux par les structures de patrons et les ontologies

Gabin Personeni , Emmanuel Bresso , Marie-Dominique Devignes , Michel Dumontier , Malika Smaïl-Tabbone et al.
Journée I.A. et Santé, Jul 2018, Nancy, France
Conference papers hal-01872312v1
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Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach

Gabin Personeni , Marie-Dominique Devignes , Malika Smaïl-Tabbone , Philippe Jonveaux , Céline Bonnet et al.
Proceedings of the 11th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018), Dec 2018, Antwerp, Belgium
Conference papers hal-01925471v1
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Using formal concept analysis for checking the structure of an ontology in LOD: the example of DBpedia

Pierre Monnin , Mario Lezoche , Amedeo Napoli , Adrien Coulet
23rd International Symposium on Methodologies for Intelligent Systems, ISMIS 2017, Warsaw university of technology, Jun 2017, Warsaw, Poland. pp.674-683, ⟨10.1007/978-3-319-60438-1_66⟩
Conference papers hal-01511909v1
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Tree-LSTM and Cross-Corpus Training for Extracting Biomedical Relationships from Text

Joël Legrand , Yannick Toussaint , Chedy Raïssi , Adrien Coulet
DLPM2017 Workshop - 2nd International Workshop on Deep Learning for Precision Medicine, Sep 2017, Skopje, Macedonia
Conference papers hal-01592802v1
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PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units

Pierre Monnin , Clement Jonquet , Joël Legrand , Amedeo Napoli , Adrien Coulet et al.
Methods, tools & platforms for Personalized Medicine in the Big Data Era, Oct 2017, Palermo, Italy. ⟨10.7287/peerj.preprints.3140v1⟩
Conference papers hal-01593184v2
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Extraction d'association d'EIM à partir de dossiers patients : expérimentation avec les structures de patrons et les ontologies

Gabin Personeni , Marie-Dominique Devignes , Michel Dumontier , Malika Smaïl-Tabbone , Adrien Coulet et al.
Deuxième Atelier sur l'Intelligence Artificielle et la Santé, Jun 2016, Montpellier, France
Conference papers hal-01391172v1
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Discovering ADE associations from EHRs using pattern structures and ontologies

Gabin Personeni , Marie-Dominique Devignes , Michel Dumontier , Malika Smaïl-Tabbone , Adrien Coulet et al.
Phenotype Day, Bio-Ontologies SIG, ISMB, Jul 2016, Orlando, United States
Conference papers hal-01369448v1
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Suggesting valid pharmacogenes by mining linked data

Kevin Dalleau , Ndeye Coumba Ndiaye , Adrien Coulet
Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2015, Dec 2015, Cambridge, United Kingdom
Conference papers hal-01239568v1
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Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs

Mohsen Hassan , Olfa Makkaoui , Adrien Coulet , Yannick Toussaint
BioNLP 15, Association for Computational Linguistics, Jul 2015, Beijing, China. pp.184
Conference papers hal-01184655v1
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Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability

Gabin Personeni , Simon Daget , Céline Bonnet , Philippe Jonveaux , Marie-Dominique Devignes et al.
Data Integration in the Life Sciences - 10th International Conference, DILS 2014, Jul 2014, Lisbon, Portugal. pp.16 - 31, ⟨10.1007/978-3-319-08590-6_2⟩
Conference papers hal-01095591v1
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ILP for Mining Linked Open Data: a biomedical Case Study

Gabin Personeni , Simon Daget , Céline Bonnet , Philippe Jonveaux , Marie-Dominique Devignes et al.
The 24th International Conference on Inductive Logic Programming (ILP 2014), Sep 2014, Nancy, France
Conference papers hal-01095597v1
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Learning Subgraph Patterns from text for Extracting Disease–Symptom Relationships

Mohsen Hassan , Adrien Coulet , Yannick Toussaint
1st International Workshop on Interactions between Data Mining and Natural Language Processing, Sep 2014, Nancy, France
Conference papers hal-01095595v1
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Using pattern structures for analyzing ontology-based annotations of biomedical data

Adrien Coulet , Florent Domenach , Mehdi Kaytoue , Amedeo Napoli
Septièmes Journées d'Intelligence Artificielle Fondamentale, Jun 2013, Aix-en-Provence, France. pp.97--106
Conference papers hal-00922392v1
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Lattice Based Data Access (LBDA): An Approach for Organizing and Accessing Linked Open Data in Biology

Mehwish Alam , Melisachew Wudage Chekol , Adrien Coulet , Amedeo Napoli , Malika Smaïl-Tabbone et al.
DMoLD'13 - Data Mining on Linked Data Workshop (ECML/PKDD, 2013), Sep 2013, Prague, Czech Republic
Conference papers hal-00903450v1
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Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data

Adrien Coulet , Florent Domenach , Mehdi Kaytoue , Amedeo Napoli
International Conference on Formal Concept Analysis, May 2013, Dresden, Germany
Conference papers hal-00880643v1
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Formal Concept Analysis Applied to Transcriptomic Data

Mehwish Alam , Adrien Coulet , Amedeo Napoli , Malika Smaïl-Tabbone
The Ninth International Conference on Concept Lattices and Their Applications - CLA 2012, Oct 2012, Fuengirola (Málaga), Spain
Conference papers hal-00761003v1
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Formal Concept Analysis Applied to Transcriptomic Data

Mehwish Alam , Adrien Coulet , Amedeo Napoli , Malika Smaïl-Tabbone
What can FCA do for Artificial Intelligence (FCA4AI) (ECAI 2012), Aug 2012, Montpellier, France
Conference papers hal-00760993v1
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NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

Clement Jonquet , Paea Lependu , Sean M. Falconer , Adrien Coulet , Natalya F. Noy et al.
Semantic Web Challenge, 9th International Semantic Web Conference, ISWC'10, Nov 2010, Shangai, China. pp.8
Conference papers hal-00557982v1
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Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical

Clement Jonquet , Adrien Coulet , Nigam Shah , Mark A. Musen
21èmes Journées Francophones d'Ingénierie des Connaissances, Jun 2010, Nimes, France. pp.271-282
Conference papers hal-00488419v1

Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics

Adrien Coulet , Malika Smail-Tabbone , Amedeo Napoli , Marie-Dominique Devignes
21st International Workshop on Description Logics - DL2008, May 2008, Dresden, Germany
Conference papers inria-00338677v1
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Ontology-guided Data Preparation for Discovering Genotype-Phenotype Relationships

Adrien Coulet , Malika Smaïl-Tabbone , Pascale Benlian , Amedeo Napoli , Marie-Dominique Devignes et al.
Network Tools and Applications in Biology: A Semantic Web for Bioinformatics - NETTAB 2007, Jun 2007, Pisa, Italy
Conference papers inria-00186988v1
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Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing

Adrien Coulet , Malika Smaïl-Tabbone , Amedeo Napoli , Marie-Dominique Devignes
Proceedings of International Workshop on Knowledge Systems in Bioinformatics - KSinBIT'06, Oct 2006, Montpellier, France
Conference papers inria-00089824v1
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SNP-Ontology for semantic integration of genomic variation data

Adrien Coulet , Malika Smaïl-Tabbone , Pascale Benlian , Amedeo Napoli , Marie-Dominique Devignes et al.
14th Annual International Conference on Intelligent Systems for Molecular Biology - ISMB'06, Aug 2006, Fortaleza/Brésil
Conference papers inria-00067863v2
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SNP-Converter: an Ontology-Based solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies

Adrien Coulet , Malika Smaïl-Tabbone , Pascale Benlian , Amedeo Napoli , Marie-Dominique Devignes et al.
3rd International Workshop on Data Integration in the Life Sciences 2006 - DILS'06, Jul 2006, European Bioinformatics Institute (EBI), Hinxton/UK
Conference papers inria-00080050v1

Ontology-driven Data Integration for Pharmacogenomics: Application to Genome Variations

Adrien Coulet , Malika Smaïl-Tabbone , Pascale Benlian , Amedeo Napoli , Marie-Dominique Devignes et al.
Journées Ouvertes : Biologie, Informatique et Mathématiques - JOBIM'06, Centre de Bioinformatique de Bordeaux (CBiB), Jul 2006, Bordeaux/France
Conference papers inria-00080064v1
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Extraction de données pharmacogénomiques à partir d'études cliniques : problématique

Adrien Coulet , Marie-Dominique Devignes , Malika Smaïl-Tabbone
Deuxième atelier sur la "Fouille de données complexes dans un processus d'extraction des connaissances", Jan 2005, Paris/France
Conference papers inria-00080156v1
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PGxCorpus and PGxLOD: two shared resources for knowledge management in pharmacogenomics

Pierre Monnin , Joël Legrand , Adrien Coulet
JOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. , JOBIM 2022 Proceedings - Posters, Démos
Conference poster hal-03754888v1
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Discovering Subsumption Axioms with Concept Annotation

Pierre Monnin , Amedeo Napoli , Adrien Coulet
BDA 2017 - 33ème Conférence sur la Gestion de Données — Principes, Technologies et Applications, Nov 2017, Nancy, France. Gestion de Données — Principes, Technologies et Applications (BDA 2017)
Conference poster hal-01671454v2
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Mining Linked Open Data: a Case Study with Genes Responsible for Intellectual Disability

Gabin Personeni , Simon Daget , Céline Bonnet , Philippe Jonveaux , Marie-Dominique Devignes et al.
ECCB'14 (European Conference on Computational Biology 2014), Sep 2014, Strasbourg, France. , 2014
Conference poster hal-01092800v1
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Ontology-based Web Services for Data Annotation and Integration

Patricia L. Whetzel , Nigam H. Shah , Natalya Noy , Clement Jonquet , Adrien Coulet et al.
ISMB: Intelligent Systems for Molecular Biology, Jul 2010, Boston, United States. , 18th International Conference on Intelligent Systems for Molecular Biology, 2010
Conference poster lirmm-01605892v1

Ontology-based knowledge discovery in pharmacogenomics.

Adrien Coulet , Malika Smaïl-Tabbone , Amedeo Napoli , Marie-Dominique Devignes
Hamid R. Arabnia and Quoc-Nam Tran. Software Tools and Algorithms for Biological Systems, 696, Springer, pp.357-66, 2011, Advances in Experimental Medicine and Biology, 978-1-4419-7046-6. ⟨10.1007/978-1-4419-7046-6_36⟩
Book sections inria-00585072v1