The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease

The American Journal of Human Genetics - Tập 83 Số 5 - Trang 610-615 - 2008
Peter N. Robinson1,2, Sebastian Köhler1,2, Sebastian Bauer2, Dominik Seelow3,2, Denise Horn2, Stefan Mundlos1,2,4
1Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
2Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
3Department of Neuropaediatrics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
4Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany

Tóm tắt

Từ khóa


Tài liệu tham khảo

Smith, 2005, The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information, Genome Biol., 6, R7, 10.1186/gb-2004-6-1-r7

Lussier, 2007, Computational approaches to phenotyping: high-throughput phenomics, Proc. Am. Thorac. Soc., 4, 18, 10.1513/pats.200607-142JG

Robinson, 2006, The molecular genetics of Marfan syndrome and related disorders, J. Med. Genet., 43, 769, 10.1136/jmg.2005.039669

Brunner, 2004, From syndrome families to functional genomics, Nat. Rev. Genet., 5, 545, 10.1038/nrg1383

Oti, 2007, The modular nature of genetic diseases, Clin. Genet., 71, 1, 10.1111/j.1399-0004.2006.00708.x

Gelb, 2006, Noonan syndrome and related disorders: Dysregulated RAS-mitogen activated protein kinase signal transduction, Hum Mol Genet, 15 Spec No 2, R220, 10.1093/hmg/ddl197

Goh, 2007, The human disease network, Proc. Natl. Acad. Sci. USA, 104, 8685, 10.1073/pnas.0701361104

Feldman, 2008, Network properties of genes harboring inherited disease mutations, Proc. Natl. Acad. Sci. USA, 105, 4323, 10.1073/pnas.0701722105

Köhler, 2008, Walking the interactome for prioritization of candidate disease genes, Am. J. Hum. Genet., 82, 949, 10.1016/j.ajhg.2008.02.013

Hamosh, 2005, Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders, Nucleic Acids Res., 33, D514, 10.1093/nar/gki033

Masseroli, 2005, Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists, BMC Bioinformatics, 6, S18, 10.1186/1471-2105-6-S4-S18

Bajdik, 2005, CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes, BMC Bioinformatics, 6, 78, 10.1186/1471-2105-6-78

van Driel, 2006, A text-mining analysis of the human phenome, Eur. J. Hum. Genet., 14, 535, 10.1038/sj.ejhg.5201585

Ashburner, 2000, Gene Ontology: tool for the unification of biology. the Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556

Day-Richter, 2007, OBO-Edit–an ontology editor for biologists, Bioinformatics, 23, 2198, 10.1093/bioinformatics/btm112

Smith, 1981, Identification of common molecular subsequences, J. Mol. Biol., 147, 195, 10.1016/0022-2836(81)90087-5

2001, Creating the Gene Ontology resource: design and implementation, Genome Res., 11, 1425, 10.1101/gr.180801

Resnik, 1995, Using information content to evaluate semantic similarity in a taxonomy, Proceedings of the 14th IJCAI, 1, 448

Pesquita, 2008, Metrics for GO based protein semantic similarity: a systematic evaluation, BMC Bioinformatics, 9, S4, 10.1186/1471-2105-9-S5-S4

Perez-Iratxeta, 2002, Association of genes to genetically inherited diseases using data mining, Nat. Genet., 31, 316, 10.1038/ng895

Hristovski, 2005, Using literature-based discovery to identify disease candidate genes, Int. J. Med. Inform., 74, 289, 10.1016/j.ijmedinf.2004.04.024

Lage, 2007, A human phenome-interactome network of protein complexes implicated in genetic disorders, Nat. Biotechnol., 25, 309, 10.1038/nbt1295

Bodenreider, 2002, Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics, Proc AMIA Symp, 61

Grossmann, 2007, Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis, Bioinformatics, 23, 3024, 10.1093/bioinformatics/btm440

Lu, 2008, A probabilistic generative model for GO enrichment analysis, Nucleic Acids Res., 36, e109, 10.1093/nar/gkn434

Smith, 2007, The OBO foundry: coordinated evolution of ontologies to support biomedical data integration, Nat. Biotechnol., 25, 1251, 10.1038/nbt1346

Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303

Maslov, 2002, Specificity and stability in topology of protein networks, Science, 296, 910, 10.1126/science.1065103