{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T17:02:20Z","timestamp":1742403740025},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2875,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Computational methods are widely used to discover gene\u2013disease relationships hidden in vast masses of available genomic and post-genomic data. In most current methods, a similarity measure is calculated between gene annotations and known disease genes or disease descriptions. However, more explicit gene\u2013disease relationships are required for better insights into the molecular bases of diseases, especially for complex multi-gene diseases.<\/jats:p>\n               <jats:p>Results: Explicit relationships between genes and diseases are formulated as candidate gene definitions that may include intermediary genes, e.g. orthologous or interacting genes. These definitions guide data modelling in our database approach for gene\u2013disease relationship discovery and are expressed as views which ultimately lead to the retrieval of documented sets of candidate genes. A system called ACGR (Approach for Candidate Gene Retrieval) has been implemented and tested with three case studies including a rare orphan gene disease.<\/jats:p>\n               <jats:p>Availability: The ACGR sources are freely available at http:\/\/bioinfo.loria.fr\/projects\/acgr\/acgr-software\/. See especially the file \u2018disease_description\u2019 and the folders \u2018Xcollect_scenarios\u2019 and \u2018ACGR_views\u2019.<\/jats:p>\n               <jats:p>Contact: \u00a0devignes@loria.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn612","type":"journal-article","created":{"date-parts":[[2008,11,29]],"date-time":"2008-11-29T01:13:20Z","timestamp":1227921200000},"page":"230-236","source":"Crossref","is-referenced-by-count":20,"title":["Gene\u2013disease relationship discovery based on model-driven data integration and database view definition"],"prefix":"10.1093","volume":"25","author":[{"given":"S.","family":"Yilmaz","sequence":"first","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]},{"given":"P.","family":"Jonveaux","sequence":"additional","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]},{"given":"C.","family":"Bicep","sequence":"additional","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]},{"given":"L.","family":"Pierron","sequence":"additional","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]},{"given":"M.","family":"Sma\u00efl-Tabbone","sequence":"additional","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]},{"given":"M.D.","family":"Devignes","sequence":"additional","affiliation":[{"name":"1 Laboratory for Human Genetics, Nancy Medical Faculty, rue du Morvan, 54500 Vandoeuvre-les-Nancy cedex and 2LORIA UMR7503, CNRS, INRIA, Nancy-Universit\u00e9, BP239, 54506 Vandoeuvre-les-Nancy cedex, France"}]}],"member":"286","published-online":{"date-parts":[[2008,11,18]]},"reference":[{"key":"2023013109594779900_B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1471-2105-6-55","article-title":"Speeding disease gene discovery by sequence based candidate prioritization","volume":"6","author":"Adie","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023013109594779900_B2","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/bioinformatics\/btk031","article-title":"SUSPECTS: enabling fast and effective prioritization of positional candidates","volume":"22","author":"Adie","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013109594779900_B3","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nbt1203","article-title":"Gene prioritization through genomic data fusion","volume":"24","author":"Aerts","year":"2006","journal-title":"Nat. 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