{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T19:47:24Z","timestamp":1760384844323},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"S4","license":[{"start":{"date-parts":[[2008,4,1]],"date-time":"2008-04-01T00:00:00Z","timestamp":1207008000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,4]]},"DOI":"10.1186\/1471-2105-9-s4-s3","type":"journal-article","created":{"date-parts":[[2008,4,25]],"date-time":"2008-04-25T18:14:06Z","timestamp":1209147246000},"source":"Crossref","is-referenced-by-count":12,"title":["Ontology-guided data preparation for discovering genotype-phenotype relationships"],"prefix":"10.1186","volume":"9","author":[{"given":"Adrien","family":"Coulet","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malika","family":"Sma\u00efl-Tabbone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pascale","family":"Benlian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amedeo","family":"Napoli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Dominique","family":"Devignes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,4,25]]},"reference":[{"key":"2596_CR1","first-page":"1","volume-title":"Knowledge Discovery in Databases","author":"W Frawley","year":"1991","unstructured":"Frawley W, Piatetsky-Shapiro G, Matheus C: Knowledge Discovery in Databases: An Overview. In Knowledge Discovery in Databases. Edited by: Piatetsky-Shapiro G, Frawley WJ. Cambridge: AAAI\/MIT Press; 1991:1\u201330."},{"key":"2596_CR2","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1006\/knac.1993.1008","volume":"5","author":"TR Gruber","year":"1993","unstructured":"Gruber TR: A Translation Approach to Portable Ontology Specifications. Knowledge Acquisition 1993, 5: 199\u2013220.","journal-title":"Knowledge Acquisition"},{"issue":"3","key":"2596_CR3","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1093\/bib\/bbl027","volume":"7","author":"O Bodenreider","year":"2006","unstructured":"Bodenreider O, Stevens R: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 2006, 7(3):256\u2013274.","journal-title":"Briefings in Bioinformatics"},{"key":"2596_CR4","unstructured":"Bioportal [ http:\/\/www.bioontology.org\/tools\/portal\/bioportal.html ]"},{"issue":"2","key":"2596_CR5","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1089\/omi.2006.10.185","volume":"10","author":"DL Rubin","year":"2006","unstructured":"Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA: National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. OMICS 2006, 10(2):185\u2013198.","journal-title":"OMICS"},{"key":"2596_CR6","first-page":"37","volume-title":"Proceedings of the Conference on Information and Knowledge Management: 29 November \u2013 02 December 1995; Baltimore","author":"S Anand","year":"1995","unstructured":"Anand S, Bell D, Hughes J: The Role of Domain Knowledge in Data Mining. In Proceedings of the Conference on Information and Knowledge Management: 29 November \u2013 02 December 1995; Baltimore. New-York: ACM; 1995:37\u201343."},{"key":"2596_CR7","volume-title":"Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies: 24 September 2004; Pisa","author":"H Cespivova","year":"2004","unstructured":"Cespivova H, Rauch J, Svatek V, Kejkula M, Tomeckova M: Roles of Medical Ontology in Association Mining CRISP-DM Cycle. Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies: 24 September 2004; Pisa 2004."},{"key":"2596_CR8","volume-title":"Proceedings of the 8th Pacific Rim International Conference on Artificial Intelligence: 9-13 August 2004; Auckland","author":"P Gottgtroy","year":"2004","unstructured":"Gottgtroy P, Kasabov N, MacDonell S: An ontology driven approach for knowledge discovery in biomedicine. In Proceedings of the 8th Pacific Rim International Conference on Artificial Intelligence: 9\u201313 August 2004; Auckland. Berlin: Springer; 2004."},{"key":"2596_CR9","volume-title":"Proceedings of the Conference on Concept Lattices and their Applications: 30 October \u2013 1 November; Hammamet","author":"A Napoli","year":"2006","unstructured":"Napoli A: Elements on KDDK: Knowledge Discovery guided by Domain Knowledge. Proceedings of the Conference on Concept Lattices and their Applications: 30 October \u2013 1 November; Hammamet 2006."},{"key":"2596_CR10","unstructured":"OWL Web Ontology Language Overview [ http:\/\/www.w3.org\/TR\/owl-features\/ ]"},{"key":"2596_CR11","first-page":"53","volume-title":"Proceedings of the ECML\/PKDD07 Workshop Prior Conceptual Knowledge in Machine LEarning and Data Mining: 21 September; Warsaw","author":"F Karel","year":"2007","unstructured":"Karel F, Kl\u00e9ma J: Quantitative association rule mining in genomics using apriori knowledge. Proceedings of the ECML\/PKDD07 Workshop Prior Conceptual Knowledge in Machine LEarning and Data Mining: 21 September; Warsaw 2007, 53\u201364."},{"key":"2596_CR12","volume-title":"Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies: 24 September 2004; Pisa","author":"Z Nazeri","year":"2004","unstructured":"Nazeri Z, Bloedorn E: Exploiting Available Domain Knowledge to Improve Mining Aviation Safety and Network Security Data. Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies: 24 September 2004; Pisa 2004."},{"key":"2596_CR13","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1109\/5254.889106","volume":"15","author":"B Liu","year":"2000","unstructured":"Liu B, Hsu W, Chen S, Ma Y: Analyzing the subjective interestingness of association rules. IEEE Intellgent Systems 2000, 15: 47\u201355.","journal-title":"IEEE Intellgent Systems"},{"key":"2596_CR14","first-page":"407","volume-title":"Proceedings of the 21th Very Large Data Bases Conference 8-10 September 1995; Zurich","author":"R Srikant","year":"1995","unstructured":"Srikant R, Agrawal R: Mining generalized association rules. Proceedings of the 21th Very Large Data Bases Conference 8\u201310 September 1995; Zurich 1995, 407\u2013419."},{"key":"2596_CR15","volume-title":"Proceeding of the ECML\/PKDD05 Workshop on Knowledge Discovery and Ontologies: 7 October 2005; Porto","author":"V Svatek","year":"2005","unstructured":"Svatek V, Rauch J, Flek M: Ontology-Based Explanation of Discovered Associations in the Domain of Social Reality. Proceeding of the ECML\/PKDD05 Workshop on Knowledge Discovery and Ontologies: 7 October 2005; Porto 2005."},{"key":"2596_CR16","volume-title":"Data Mining: Concepts and Techniques","author":"J Han","year":"2000","unstructured":"Han J, Kamber M: Data Mining: Concepts and Techniques. San-Francisco: Morgan Kaufmann Publishers; 2000."},{"key":"2596_CR17","first-page":"532","volume":"40","author":"CA Goble","year":"2001","unstructured":"Goble CA, Stevens R, Ng G, Bechhofer S, Paton NW, Baker PG, Peim M, Brass A: Transparent Access to Multiple Bioinformatics Information Sources. IBM Systems Journal Special issue on deep computing for the life sciences 2001, 40: 532\u2013551.","journal-title":"IBM Systems Journal Special issue on deep computing for the life sciences"},{"issue":"18","key":"2596_CR18","doi-asserted-by":"publisher","first-page":"2420","DOI":"10.1093\/bioinformatics\/btg340","volume":"19","author":"J K\u00f6hler","year":"2003","unstructured":"K\u00f6hler J, Philippi S, Lange M: SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 2003, 19(18):2420\u20137.","journal-title":"Bioinformatics"},{"key":"2596_CR19","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1007\/11799511_8","volume-title":"Proceedings of the Workshop on Data Integration in the Life Sciences 20-22 July 2006; Hinxton","author":"A Coulet","year":"2006","unstructured":"Coulet A, Sma\u00efl-Tabbone M, Benlian P, Napoli A, Devignes MD: SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions. In Proceedings of the Workshop on Data Integration in the Life Sciences 20\u201322 July 2006; Hinxton. Berlin: Springer; 2006:82\u201393. LNBI 4075"},{"key":"2596_CR20","first-page":"262","volume-title":"Proceedings of the International Symposium on Medical Data Analysis 7-8 December; Thessaloniki","author":"D P\u00e9rez-Rey","year":"2006","unstructured":"P\u00e9rez-Rey D, Anguita A, Crespo J: OntoDataClean: Ontology-Based Integration and Preprocessing of Distributed Data. In Proceedings of the International Symposium on Medical Data Analysis 7\u20138 December; Thessaloniki. Berlin: Springer; 2006:262\u2013272. LNBI 4345"},{"key":"2596_CR21","volume-title":"Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies 24 September 2004; Pisa","author":"T Euler","year":"2004","unstructured":"Euler T, Scholz M: Using Ontologies in a KDD Workbench. Proceedings of the ECML\/PKDD04 Workshop on Knowledge Discovery and Ontologies 24 September 2004; Pisa 2004."},{"key":"2596_CR22","first-page":"506","volume-title":"Proceedings of the Very Large Data Bases Conference 03 \u2013 06 September 1996; Bombay","author":"S Agarwal","year":"1996","unstructured":"Agarwal S, Agrawal R, Deshpande P, Gupta A, Naughton J, Ramakrishnan R, Sarawagi S: On the Computation of Multidimensional Aggregates. In Proceedings of the Very Large Data Bases Conference 03 \u2013 06 September 1996; Bombay. San-Francisco: Morgan Kaufmann Publishers Inc.; 1996:506\u2013521."},{"key":"2596_CR23","first-page":"157","volume-title":"Proceedings of the AAAI Workshop on Knowledge Discovery in Databases 31 July \u2013 4 August 1994; Seattle","author":"J Han","year":"1994","unstructured":"Han J, Fu Y: Dynamic Generation and Refinement of Concept Hierarchies for Knowledge Discovery in Databases. In Proceedings of the AAAI Workshop on Knowledge Discovery in Databases 31 July \u2013 4 August 1994; Seattle. AAAI Press; 1994:157\u2013168."},{"key":"2596_CR24","first-page":"153","volume":"1","author":"J Han","year":"2005","unstructured":"Han J: Feature selection based on rough set and information entropy. Proceedings of the IEEE International Conference on Granular Computing: 25\u201327 July 2005; Beijing 2005, 1: 153\u2013158.","journal-title":"Proceedings of the IEEE International Conference on Granular Computing: 25-27 July 2005; Beijing"},{"key":"2596_CR25","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/S0004-3702(97)00043-X","volume":"97","author":"R Kohavi","year":"1997","unstructured":"Kohavi R, John GH: Wrappers for feature subset selection. Artificial Intelligence 1997, 97: 273\u2013324.","journal-title":"Artificial Intelligence"},{"key":"2596_CR26","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1109\/TKDE.2005.67","volume":"17","author":"A Bernstein","year":"2005","unstructured":"Bernstein A, Provost F, Hill S: Toward intelligent assistance for a data mining process an ontology-based approach for cost-sensitive classification. IEEE Transactions on Knowledge and Data Engineering 2005, 17: 503\u2013518.","journal-title":"IEEE Transactions on Knowledge and Data Engineering"},{"key":"2596_CR27","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1093\/bioinformatics\/19.1.79","volume":"19","author":"C Creighton","year":"2003","unstructured":"Creighton C, Hanash S: Mining gene expression databases for association rules. Bioinformatics 2003, 19: 79\u201386.","journal-title":"Bioinformatics"},{"key":"2596_CR28","doi-asserted-by":"publisher","first-page":"ii54","DOI":"10.1093\/bioinformatics\/bti1109","volume":"21","author":"E Capriotti","year":"2005","unstructured":"Capriotti E, Fariselli P, Calabrese R, Casadio R: Predicting Protein Stability Changes from Sequences Using Support Vector Machines. Bioinformatics 2005, 21: ii54-ii58.","journal-title":"Bioinformatics"},{"key":"2596_CR29","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/1471-2105-7-258","volume":"7","author":"J Li","year":"2006","unstructured":"Li J, Zhou Y, Elston RC: Haplotype-based Quantitative Trait Mapping Using a Clustering Algorithm. BMC Bioinformatics 2006, 7: 258.","journal-title":"BMC Bioinformatics"},{"key":"2596_CR30","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1111\/j.1399-0004.2006.00628.x","volume":"70","author":"MCY Ng","year":"2006","unstructured":"Ng MCY, Baum L, So WY, Lam VKL, Wang Y, Poon E, Tomlinson B, Cheng S, Lindpaintner K, Chan JCN: Association of lipoprotein lipase S447X, apolipoprotein E exon 4, and apoC3 -455T-C polymorphisms on the susceptibility to diabetic nephropathy. Clin Genet 2006, 70: 20\u201328.","journal-title":"Clin Genet"},{"issue":"3","key":"2596_CR31","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/sj.clpt.6100087","volume":"81","author":"KM Giacomini","year":"2007","unstructured":"Giacomini KM, Brett CM, Altman RB, et al.: The pharmacogenetics research network from SNP discovery to clinical drug response. Clin Pharmacol Ther 2007, 81(3):328\u201345.","journal-title":"Clin Pharmacol Ther"},{"key":"2596_CR32","unstructured":"HapMap [ http:\/\/www.hapmap.org\/ ]"},{"issue":"2","key":"2596_CR33","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","volume":"21","author":"JC Barrett","year":"2005","unstructured":"Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263\u20135.","journal-title":"Bioinformatics"},{"issue":"1","key":"2596_CR34","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1038\/nsmb873","volume":"12","author":"ML Hastings","year":"2005","unstructured":"Hastings ML, Resta N, Traum D, Stella A, Guanti G, Krainer AR: An LKB1 AT-AC intron mutation causes Peutz-Jeghers syndrome via splicing at noncanonical cryptic splice sites. Nat Struct Mol Biol 2005, 12(1):54\u201359.","journal-title":"Nat Struct Mol Biol"},{"key":"2596_CR35","unstructured":"SNP-Ontology [ http:\/\/www.bioontology.org\/files\/6723\/snpontology_full.owl ]"},{"key":"2596_CR36","unstructured":"WayStation [ http:\/\/www.centralmutations.org\/ ]"},{"key":"2596_CR37","unstructured":"SO-Pharm [ http:\/\/www.obofoundry.org\/cgi-bin\/detail.cgi?id=pharmacogenomics ]"},{"key":"2596_CR38","first-page":"648","volume-title":"Proceedings of the Wokshop on Knowledge Systems in Bioinformatics 29 October 2006; Montpellier","author":"A Coulet","year":"2006","unstructured":"Coulet A, Sma\u00efl-Tabbone M, Napoli A, Devignes MD: Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. In Proceedings of the Wokshop on Knowledge Systems in Bioinformatics 29 October 2006; Montpellier. Berlin: Springer; 2006:648\u201357. LNCS 4277"},{"key":"2596_CR39","unstructured":"Open Biomedical Ontologies (OBO) Foundry [ http:\/\/obofoundry.org ]"},{"key":"2596_CR40","volume-title":"Proceedings of the Third International Semantic Web Conference 7-11 November 2004; Hiroshima","author":"H Knublauch","year":"2004","unstructured":"Knublauch H, Fergerson RW, Noy NF, Musen MA: The Prot\u00e9g\u00e9 OWL Plugin: An Open Development Environment for Semantic Web Applications. In Proceedings of the Third International Semantic Web Conference 7\u201311 November 2004; Hiroshima. Berlin: Springer; 2004."},{"key":"2596_CR41","volume-title":"Proceedings of the WWW2001 Workshop on the Semantic Web 1 May 2001; Hong Kong","author":"B McBride","year":"2001","unstructured":"McBride B: Jena: Implementing the RDF Model and Syntax Specification. Proceedings of the WWW2001 Workshop on the Semantic Web 1 May 2001; Hong Kong 2001."},{"key":"2596_CR42","volume-title":"Proceedings of the Workshop on Description Logics 6-8 June 2004; Whistler","author":"E Sirin","year":"2004","unstructured":"Sirin E, Parsia B: Pellet: An OWL DL Reasoner. Proceedings of the Workshop on Description Logics 6\u20138 June 2004; Whistler 2004."},{"key":"2596_CR43","unstructured":"Prot\u00e9g\u00e9 4 alpha plugins [ http:\/\/www.co-ode.org\/downloads\/protege-x\/plugins.php ]"},{"issue":"2","key":"2596_CR44","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1145\/170036.170072","volume":"22","author":"R Agrawal","year":"1993","unstructured":"Agrawal R, Imielinski T, Swami AN: Mining Association Rules between Sets of Items in Large Databases. SIGMOD 1993, 22(2):207.","journal-title":"SIGMOD"},{"key":"2596_CR45","volume-title":"Proceedings of the 5th International Conference on Concept Lattices and Their Applications 24-26 October 2007; Montpellier","author":"L Szathmary","year":"2007","unstructured":"Szathmary L, Napoli A, Kuznetsov SO: ZART: A Multifunctional Itemset Mining Algorithm. Proceedings of the 5th International Conference on Concept Lattices and Their Applications 24\u201326 October 2007; Montpellier 2007."},{"key":"2596_CR46","first-page":"139","volume":"2","author":"DH Fisher","year":"1987","unstructured":"Fisher DH: Knowledge Acquisition via Incremental Conceptual Clustering. Machine Learning 1987, 2: 139\u2013172.","journal-title":"Machine Learning"},{"key":"2596_CR47","first-page":"110","volume-title":"Supplementary Proceedings of the Third International Conference on Formal Concept Analysis 14-18 February; Lens","author":"L Szathmary","year":"2005","unstructured":"Szathmary L, Napoli A: CORON: A Framework for Levelwise Itemset Mining Algorithms. Supplementary Proceedings of the Third International Conference on Formal Concept Analysis 14\u201318 February; Lens 2005, 110\u2013113."},{"key":"2596_CR48","volume-title":"Data Mining Practical machine learning tools and techniques","author":"IH Witten","year":"2005","unstructured":"Witten IH, Frank E: Data Mining Practical machine learning tools and techniques. San-Francisco: Morgan Kaufmann Publishers; 2005."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-S4-S3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-S4-S3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-S4-S3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,4]],"date-time":"2020-05-04T20:01:28Z","timestamp":1588622488000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-S4-S3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4]]},"references-count":48,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2008,4]]}},"alternative-id":["2596"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-s4-s3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,4]]},"article-number":"S3"}}