. Bibliographie-[abele, Linking Open Data cloud diagram, 2017.

. Agrawal, Mining association rules between sets of items in large databases, Acm sigmod record, vol.22, p.207216, 1993.

. Agrawal, Fast algorithms for mining association rules, Proc. 20th int. conf. very large data bases, VLDB, vol.1215, p.487499, 1994.

. Aït-kaci, Ecient implementation of lattice operations, ACM Transactions on Programming Languages and Systems (TOPLAS), vol.11, issue.1, p.115146, 1989.

A. , Bridging dbpedia categories and dl-concept denitions using formal concept analysis, FCA4AI 2015, co-located with the International Joint Conference on Articial Intelligence (IJCAI 2015), p.1430, 2015.

, International classication of diseases, 9th revision, clinical modication : physician ICD-9-CM, 2005 : volumes 1 and 2, color-coded, illustrated, vol.1, 2004.

. Antezana, Biological knowledge management : the emerging role of the Semantic Web technologies, Briengs in Bioinformatics, vol.10, issue.4, p.392407, 2009.

A. R. Aronson-;-aronson, Eective mapping of biomedical text to the umls metathesaurus : the metamap program, Proceedings of the AMIA Symposium, p.17, 2001.

. Ashburner, Gene Ontology : tool for the unication of biology, Nature genetics, vol.25, issue.1, p.2529, 2000.

F. Baader-;-baader, The description logic handbook : Theory, implementation and applications, 2003.

[. Baader, Description logics as ontology languages for the semantic web, Mechanizing Mathematical Reasoning, p.228248, 2005.

[. Banda, A curated and standardized adverse drug event resource to accelerate drug safety research, p.3, 2016.

[. Bibliographie and . Barabási, Network medicine : a network-based approach to human disease, Nature reviews genetics, vol.12, issue.1, p.56, 2011.

[. Barrell, The GOA database in 2009an integrated Gene Ontology Annotation resource, Nucleic Acids Research, vol.37, issue.1, p.396403, 2009.

B. Beckett, D. Beckett, and T. Berners-lee, Turtle-Terse RDF Triple Language, 2011.

[. Belleau, Bio2RDF : Towards a mashup to build bioinformatics knowledge systems, Journal of Biomedical Informatics, vol.41, issue.5, pp.706-716, 2008.

[. Benabderrahmane, Intelligo : a new vector-based semantic similarity measure including annotation origin, BMC bioinformatics, vol.11, issue.1, p.1, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00543910

[. Bender, Lowest common ancestors in trees and directed acyclic graphs, Journal of Algorithms, vol.57, issue.2, p.7594, 2005.

T. Berners-lee-;-berners-lee, Rfc 1630. Universal Resource Identiers in WWW : A Unifying Syntax for the Expression of Names and Addresses of Objects on the Network as used in the World-Wide Web, 1994.

T. Berners-lee-;-berners-lee, Linked data-design issues, 2006.

. Berners-lee, The semantic web, Scientic american, vol.284, issue.5, p.2837, 2001.

[. Berthold, KNIME-the Konstanz information miner : version 2.0 and beyond, ACM SIGKDD explorations Newsletter, vol.11, issue.1, p.2631, 2009.

[. Berthold, Parallel Universes and Local Patterns, vol.07181, 2007.

G. Birkho, Théorie et applications des treillis, Annales de l'IHP, vol.11, p.227240, 1949.

[. Bizer, Linked Data-The Story So Far, Int. J. Semantic Web Inf. Syst, vol.5, issue.3, p.122, 2009.

O. Bodenreider, The unied medical language system (umls) : integrating biomedical terminology, Nucleic acids research, vol.32, issue.suppl_1, pp.267-270, 2004.

J. Bordat, Calcul pratique du treillis de galois d'une correspondance, Mathématiques et Sciences humaines, p.3147, 1986.

E. Bresso, Organisation et exploitation des connaissances sur les réseaux d'intéractions biomoléculaires pour l'étude de l'étiologie des maladies génétiques et la caractérisation des eets secondaires de principes actifs, 2013.

[. Callahan, Bio2RDF Release 2 : Improved Coverage, Interoperability and Provenance of Life Science Linked Data, The Semantic Web : Semantics and Big Data, vol.7882, 2013.

[. Calvanese, Tractable reasoning and ecient query answering in description logics : The dl-lite family, Journal of Automated reasoning, vol.39, issue.3, p.385429, 2007.

[. Cimiano, Conceptual knowledge processing with formal concept analysis and ontologies, International Conference on Formal Concept Analysis, p.189207, 2004.

. Clocksin, W. F. Mellish-;-clocksin, and C. S. Mellish, Programming in PROLOG, 2003.

[. Copeland, Bias due to misclassication in the estimation of relative risk, American journal of epidemiology, vol.105, issue.5, p.488495, 1977.

[. Coulet, Using pattern structures for analyzing ontology-based annotations of biomedical data, International Conference on Formal Concept Analysis, p.7691, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00880643

[. Couto, Measuring semantic similarity between gene ontology terms, Data & knowledge engineering, vol.61, issue.1, p.137152, 2007.
DOI : 10.1016/j.datak.2006.05.003

[. Cyganiak, RDF 1.1 Concepts and Abstract Syntax, 2014.

G. De, Using ontologies for semantic data integration, A Comprehensive Guide Through the Italian Database Research Over the Last 25 Years, p.187202, 2018.

D. Defays, An ecient algorithm for a complete link method, The Computer Journal, vol.20, issue.4, p.364366, 1977.
DOI : 10.1093/comjnl/20.4.364

URL : https://academic.oup.com/comjnl/article-pdf/20/4/364/1108735/200364.pdf

L. R. Dice, Measures of the amount of ecologic association between species, Ecology, vol.26, issue.3, p.297302, 1945.

K. Donnelly-;-donnelly, Snomed-ct : The advanced terminology and coding system for ehealth, Studies in health technology and informatics, vol.121, p.279, 2006.

[. Dumontier, Bio2rdf release 3 : a larger connected network of linked data for the life sciences, Proceedings of the 2014 International Conference on Posters & Demonstrations Track, vol.1272, p.401404, 2014.

J. C. Dunn-;-dunn, A fuzzy relative of the isodata process and its use in detecting compact well-separated clusters, 1973.

I. R. Edwards and J. K. Aronson, Adverse drug reactions : denitions, diagnosis, and management, The Lancet, vol.356, issue.9237, pp.1255-1259, 2000.

O. Erling-;-erling, Virtuoso, a hybrid rdbms/graph column store, IEEE Data Eng. Bull, vol.35, issue.1, p.38, 2012.

[. Euzenat, Ontology matching, vol.18, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00922291

. Fayyad, From data mining to knowledge discovery in databases. AI magazine, FDA adverse event reporting system (FAERS), vol.17, 1996.

[. Bibliographie and . Galárraga, Amie : association rule mining under incomplete evidence in ontological knowledge bases, Proceedings of the 22nd international conference on World Wide Web, p.413422, 2013.

. Gandon, F. Schreiber-;-gandon, and A. T. Schreiber, RDF 1.1 XML syntax, 2014.

K. Ganter, B. Ganter, and S. O. Kuznetsov, Pattern structures and their projections, International Conference on Conceptual Structures, p.129142, 2001.
DOI : 10.1007/3-540-44583-8_10

URL : http://www.math.tu-dresden.de/~ganter/psfiles/kuznet.ps

B. Ganter and R. Wille, Formal Concept Analysis : Mathematical Foundations, 1997.

[. Gilissen, Genome sequencing identies major causes of severe intellectual disability, Nature, vol.511, issue.7509, p.344, 2014.
DOI : 10.1038/nature13394

[. Goh, The human disease network, Proceedings of the National Academy of Sciences, vol.104, issue.21, p.86858690, 2007.

[. Goldberg, Drug-drug and drug-disease interactions in the ed : analysis of a high-risk population, The American journal of emergency medicine, vol.14, issue.5, p.447450, 1996.

. Gómez-pérez, Ontological Engineering : with examples from the areas of Knowledge Management, e-Commerce and the Semantic Web, 2006.

D. Smith, D. G. Smith, and A. J. , Adverse drug reactions, p.132157, 1984.

[. Gray, Bioschemas : From potato salad to protein annotation, International Semantic Web Conference (Posters, Demos & Industry Tracks), 2017.

[. Grimm, Ontologies and the Semantic Web, p.507579, 2011.

. Grisoni, , 2013.

, Méthodologie et outils pour l'extraction de connaissances par Programmation Logique Inductive (PLI) (Poster), 2013.

[. Guney, Networkbased in silico drug ecacy screening, Nature communications, vol.7, p.10331, 2016.

[. Hamosh, Online mendelian inheritance in man (omim), a knowledgebase of human genes and genetic disorders, Nucleic acids research, pp.514-517, 2005.

-. Hartigan, K. Y. Wong-;-hartigan-go, and J. Q. Wong, Inclusion of therapeutic failures as adverse drug reactions, Side Eects of Drugs Annual, vol.23, p.xxviixxxiii, 2000.

[. Hidalgo, , 2009.

, A dynamic network approach for the study of human phenotypes, PLoS computational biology, vol.5, issue.4, p.1000353

G. Hj, L. Hj, G. , and B. , Understanding and using the medical subject headings (mesh) vocabulary to perform literature searches, JAMA, vol.271, issue.14, p.11031108, 1994.

[. Hoehndorf, Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases, Scientic reports, vol.5, p.10888, 2015.

A. Hubert, L. Hubert, and P. Arabie, Comparing partitions, Journal of classication, vol.2, issue.1, p.193218, 1985.

[. Hunter, InterPro : the integrative protein signature database, Nucleic acids research, vol.37, issue.suppl_1, pp.211-215, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01214141

J. K. Inlow and L. L. Restifo, Molecular and comparative genetics of mental retardation, Genetics, vol.166, issue.2, p.835881, 2004.

P. Jaccard, Étude comparative de la distribution orale dans une portion des alpes et des jura, Bull Soc Vaudoise Sci Nat, vol.37, p.547579, 1901.

[. Jacomy, Forceatlas2, a continuous graph layout algorithm for handy network visualization designed for the gephi software, PloS one, vol.9, issue.6, p.98679, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01361779

D. S. Jones and . Jonquet, NCBO resource index : Ontology-based search and mining of biomedical resources, J. Web Sem, vol.9, issue.3, p.316324, 1979.

[. Jupp, The ebi rdf platform : linked open data for the life sciences, Bioinformatics, vol.30, issue.9, p.13381339, 2014.

[. Kakar, Towards pharmacovigilance using machine learning to identify unknown adverse reactions triggered by drug-drug interaction, 2016.

G. Kanehisa, M. Kanehisa, and S. Goto, Kegg : kyoto encyclopedia of genes and genomes, Nucleic acids research, vol.28, issue.1, p.2730, 2000.

[. Kaufman, The genetic basis of non-syndromic intellectual disability : a review, Journal of neurodevelopmental disorders, vol.2, issue.4, p.182, 2010.

L. Kaufman and P. Rousseeuw, Clustering by means of medoids, 1987.

R. Kaufman, L. Kaufman, and P. J. Rousseeuw, Finding groups in data : an introduction to cluster analysis, vol.344, 2009.

[. Kaytoue, Pattern structures and concept lattices for data mining and knowledge processing, Joint European Conference on Machine Learning and Knowledge Discovery in Databases, p.227231, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01188637

[. Kinjo, Protein Data Bank Japan (PDBj) : maintaining a structural data archive and resource description framework format, Nucleic Acids Research, vol.40, p.453460, 2012.

. Bibliographie-[klyne, RDF/XML Syntax Specication (Revised, 2004.

[. Knobbe, From Local Patterns to Global Models : The LeGo Approach to Data Mining, International Workshop From Local Patterns to Global Models co-located with ECML/PKDD'08, pp.1-16, 2008.

[. Knublauch, The protégé owl plugin : An open development environment for semantic web applications, The Semantic Web ISWC 2004, p.229243, 2004.

[. Köhler, The human phenotype ontology project : linking molecular biology and disease through phenotype data, Nucleic acids research, vol.42, issue.D1, pp.966-974, 2013.

R. Köpcke, H. Köpcke, and E. Rahm, Frameworks for entity matching : A comparison, Data & Knowledge Engineering, vol.69, issue.2, p.197210, 2010.

S. Kosub, A note on the triangle inequality for the jaccard distance, 2016.

[. Kourie, , 2009.

, An incremental algorithm to construct a lattice of set intersections, Science of Computer Programming, vol.74, issue.3, p.128142

[. Kuhn, The SIDER database of drugs and side eects, Nucleic acids research, p.1075, 2015.

S. Lakhal, L. Lakhal, and G. Stumme, Ecient mining of association rules based on formal concept analysis, Formal Concept Analysis, Foundations and Applications, p.180195, 2005.

[. Langfelder, Dening clusters from a hierarchical cluster tree : the dynamic tree cut package for r, Bioinformatics, vol.24, issue.5, p.719720, 2007.

[. Lauderdale, Epidemiologic uses of medicare data, Epidemiologic Reviews, vol.15, issue.2, p.319327, 1993.

[. Lependu, Pharmacovigilance using clinical notes, Clinical pharmacology & therapeutics, vol.93, issue.6, p.547555, 2013.

L. Louët, A qualitative approach to signal mining in pharmacovigilance using formal concept analysis, Studies in health technology and informatics, vol.160, p.969973, 2009.

. Lin, An information-theoretic denition of similarity, Icml, vol.98, p.296304, 1998.

F. A. Lisi, Building rules on top of ontologies for the semantic web with inductive logic programming, Theory and Practice of Logic Programming, vol.8, issue.3, p.271300, 2008.

S. Lloyd-;-lloyd, Least squares quantization in pcm, IEEE transactions on information theory, vol.28, p.129137, 1982.

[. Lord, Investigating semantic similarity measures across the gene ontology : the relationship between sequence and annotation, Bioinformatics, vol.19, issue.10, p.12751283, 2003.

[. Lowe, , 2009.

, Implications partielles dans un contexte. Mathématiques, informatique et sciences humaines, vol.29, p.3555, 1991.

[. Macqueen, Some methods for classication and analysis of multivariate observations, Proceedings of the fth Berkeley symposium on mathematical statistics and probability, vol.1, p.281297, 1967.

[. Manda, Cross-ontology multi-level association rule mining in the gene ontology, PloS one, vol.7, issue.10, p.47411, 2012.

W. ;. Mann, H. B. Mann, and D. R. Whitney, On a test of whether one of two random variables is stochastically larger than the other. The annals of mathematical statistics, p.5060, 1947.

M. Masse-;-masse, REST API Design Rulebook : Designing Consistent RESTful Web Service Interfaces, 2011.

[. Mccray, Lexical methods for managing variation in biomedical terminologies, Proceedings of the Annual Symposium on Computer Application in Medical Care, p.235, 1994.

D. L. Mcguinness, Ontologies come of age. Spinning the semantic web : bringing the World Wide Web to its full potential, p.171194, 2002.

[. Meyboom, Principles of signal detection in pharmacovigilance, Drug safety, vol.16, issue.6, p.355365, 1997.

[. Mitchell, , 1994.

, Using medicare claims for outcomes research, Medical care, pp.38-51

S. Muggleton, Inductive Logic Programming, New Generation Computing, vol.8, issue.4, p.295318, 1991.

S. Muggleton-and-raedt-;-muggleton and L. D. Raedt, Inductive logic programming : Theory and methods, The Journal of Logic Programming, vol.19, issue.20, p.629679, 1994.

[. Müller, Textpresso : an ontology-based information retrieval and extraction system for biological literature, PLoS biology, vol.2, issue.11, p.309, 2004.

[. Mungall, k-boom : A bayesian approach to ontology structure inference, p.48843, 2016.

[. Mungall, , p.141, 2017.

M. A. Bibliographie, The monarch initiative : an integrative data and analytic platform connecting phenotypes to genotypes across species, Nucleic Acids Research, vol.45, issue.D1, pp.712-722, 2017.

, Gene Help : Integrated Access to Genes of Genomes in the Reference Sequence Collection, National Center for Biotechnology Information, 2005.

. Noy, The ontology life cycle : Integrated tools for editing, publishing, peer review, and evolution of ontologies, AMIA Annual Symposium Proceedings, vol.2010, p.552, 2010.

. Noy, Bioportal : ontologies and integrated data resources at the click of a mouse, Nucleic Acids Research, vol.37, issue.2, pp.170-173, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00492020

[. Pasquier, Ecient mining of association rules using closed itemset lattices, Information systems, vol.24, issue.1, p.2546, 1999.

. Pearson and K. Pearson, Notes on regression and inheritance in the case of two parents, Proceedings of the Royal Society of London, vol.58, p.240242, 1895.

[. Pesquita, Evaluating go-based semantic similarity measures, Proc. 10th Annual Bio-Ontologies Meeting, vol.37, p.38, 2007.

[. Poggi, Linking data to ontologies, Journal on data semantics X, p.133173, 2008.

[. Prud, Objective criteria for the evaluation of clustering methods, Journal of the American Statistical association, vol.66, issue.336, p.846850, 1971.

T. Rawlins, M. Rawlins, and J. Thompson, Pathogenesis of adverse drug reactions, 1977.

T. Rawlins, M. Rawlins, and J. Thompson, Pathogenesis of adverse drug reactions, 1981.

[. Razick, iRefIndex : a consolidated protein interaction database with provenance, BMC bioinformatics, vol.9, issue.1, p.405, 2008.

P. Resnik, Using information content to evaluate semantic similarity in a taxonomy, 1995.

[. Resnik, Semantic similarity in a taxonomy : An informationbased measure and its application to problems of ambiguity in natural language, J. Artif. Intell. Res.(JAIR), vol.11, p.95130, 1999.

R. , The human phenotype ontology : A tool for annotating and analyzing human hereditary disease, The American Journal of Human Genetics, vol.83, issue.5, p.615, 2008.

. Rodríguez-lópez, Phenuma : a tool for integrating the biomedical relationships among genes and diseases, BMC bioinformatics, vol.15, issue.1, p.375, 2014.

[. Roitmann, Patient stratication and identication of adverse event correlations in the space of 1190 drug related adverse events, Frontiers in physiology, vol.5, 2014.

L. Rokach and O. Maimon, Clustering methods. In Data mining and knowledge discovery handbook, p.321352, 2005.

R. J. Royer-;-royer, Mechanism of action of adverse drug reactions : an overview, Pharmacoepidemiology and drug safety, vol.6, issue.S3, 1997.

. Rubin, Biomedical ontologies : a functional perspective, Briengs in bioinformatics, vol.9, issue.1, p.7590, 2007.

[. Sakaeda, Data mining of the public version of the fda adverse event reporting system, Int J Med Sci, vol.10, issue.7, p.796, 2013.

[. Samwald, Linked open drug data for pharmaceutical research and development, J. Cheminformatics, vol.3, p.19, 2011.

[. Schedlbauer, What evidence supports the use of computerized alerts and prompts to improve clinicians' prescribing behavior, Journal of the American Medical Informatics Association, vol.16, issue.4, p.531538, 2009.

[. Schlicker, A new measure for functional similarity of gene products based on gene ontology, BMC bioinformatics, vol.7, issue.1, p.302, 2006.

. Schmachtenberg, State of the LOD Cloud, 2014.

. Schriml, Disease ontology : a backbone for disease semantic integration, Nucleic acids research, vol.40, issue.D1, pp.940-946, 2011.

[. Sevilla, Correlation between gene expression and go semantic similarity, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, issue.4, p.330338, 2005.

R. Sibson, Slink : an optimally ecient algorithm for the single-link cluster method, The computer journal, vol.16, issue.1, p.3034, 1973.

. Singhal, Modern information retrieval : A brief overview, IEEE Data Eng. Bull, vol.24, issue.4, p.3543, 2001.

[. Spasic, Text mining and ontologies in biomedicine : Making sense of raw text, Briengs in Bioinformatics, vol.6, issue.3, p.239251, 2005.

M. Stumme, G. Stumme, and A. Maedche, Fca-merge : Bottom-up merging of ontologies, IJCAI, vol.1, p.225230, 2001.

A. Tversky, Features of similarity, Psychological review, vol.84, issue.4, 1977.

. Bibliographie, UniProt : the universal protein knowledgebase, Nucleic acids research, vol.45, issue.D1, pp.158-169, 2016.

, UMLS R Reference Manual, 2009.

U. S. Nlm, MEDLINE R /PubMed R Resources Guide, 2018.

[. Valtchev, Galicia : an open platform for lattices, Using Conceptual Structures : Contributions to the 11th Intl. Conference on Conceptual Structures (ICCS'03), p.241254, 2003.

. Van-der-merwe, Treatable inborn errors of metabolism causing intellectual disability : a systematic literature review, International Conference on Formal Concept Analysis, vol.105, p.368381, 2004.

G. Vasudevan, A. R. Vasudevan, and E. M. Ginzler, Established and novel treatments for lupus : agents in clinical trials are targeting various immunological processes, The Journal of Musculoskeletal Medicine, vol.26, issue.8, p.291291, 2009.

[. Villerd, Adverse drug reaction mining in pharmacovigilance data using formal concept analysis, Joint European Conference on Machine Learning and Knowledge Discovery in Databases, p.386401, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00599549

, OWL 2 Web Ontology Language Document Overview, 2012.

M. J. Warrens, On the equivalence of cohen's kappa and the hubertarabie adjusted rand index, Journal of Classication, vol.25, issue.2, p.177183, 2008.

[. Wheeler, Database resources of the national center for biotechnology information, vol.35, pp.5-12, 2007.

[. Whetzel, BioPortal : enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications, Nucleic acids research, vol.39, issue.2, pp.541-545, 2011.

, International statistical classication of diseases and related health problems, World Health Organization, vol.1, 2004.

, Guidelines for ATC classication and DDD assignment 16th edition. World Health Organisation Collaborating Centre for Drug Statistics Methodology, 2011.

F. Wilcoxon, Individual comparisons by ranking methods, Biometrics bulletin, vol.1, issue.6, p.8083, 1945.

[. Wilkinson, The fair guiding principles for scientic data management and stewardship, p.3, 2016.

[. Winnenburg, Exploring adverse drug events at the class level, Journal of Biomedical Semantics, vol.6, issue.1, p.18, 2015.

P. ;. Wu, Z. Wu, and M. Palmer, Verbs semantics and lexical selection, Proceedings of the 32nd annual meeting on Association for Computational Linguistics, p.133138, 1994.

[. Zhou, Human symptomsdisease network, Nature communications, vol.5, p.4212, 2014.

[. Zou, A fast incremental algorithm for constructing concept lattices, Expert Systems with Applications, vol.42, issue.9, p.44744481, 2015.