Integration of global resources for human genetic variation and disease

Human Mutation

Volumn 33, Issue 5, 2012, Pages 813-816

  Schofield, Paul N ^a   Hancock, John M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Database; Ontology; Phenotype; Precision medicine; Variation

Indexed keywords

ARTICLE; AUTOMATION; BIOINFORMATICS; FUNDING; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC DISORDER; GENETIC VARIABILITY; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN GENETICS; INTERNATIONAL COOPERATION; PHENOTYPE; PRIORITY JOURNAL; ANIMAL; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETIC SCREENING; INFORMATION DISSEMINATION; KNOWLEDGE BASE; NOMENCLATURE;

ANIMALS; DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENETIC VARIATION; HUMANS; INFORMATION DISSEMINATION; INTERNATIONAL COOPERATION; KNOWLEDGE BASES; TERMINOLOGY AS TOPIC;

EID: 84864360933     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22079     Document Type: Article

References (35)

1. 1000 Genomes Consortium. 2010. Amap of humangenome variation frompopulationscale sequencing. Nature 467:1061-1073.
2. Abbott A. 2010. Mouse project to find each gene's role. Nature 465:410.
3. Amberger J, Bocchini C, Hamosh A. 2011. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM). Hum Mutat 32(5):564-567.
4. Becker KG, Barnes KC, Bright TJ, Wang SA. 2004. The genetic association database. Nat Genet 36(5):431-432.
5. Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT. 2011. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39(Database issue):D842-D848.
6. Brown S, Moore M, 2012. Towards an encyclopedia of mammalian gene function-the International Mouse Phenotyping consortium. Dis Model Mech(in press).
7. Chen CK, Mungall CJ, Gkoutos GV, Doelken SC, Kohler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield P, Smedley D. 2012. Mouse Finder: candidate disease genes from mouse phenotype data. Hum Mutat 33:858-866.
8. Committee on a Framework for Development a New Taxonomy of Disease National Research Council. 2011. Toward precision medicine: building a knowledge network for biomedical research and a new taxonomy of disease. Washington, DC: The National Academies Press.
9. Espinosa O, Hancock JM. 2011. A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. PLo S One 6:e19693.
10. Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. 2009. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am JHum Genet 84:524-533.
11. Firth HV, Wright CF. 2011. The deciphering developmental disorders (DDD) study. Dev Med Child Neurol 53:702-703.
12. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN. 2009. Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc 2009:7069-7072.
13. Hoehndorf R, Schofield PN, Gkoutos GV. 2011. Phenome NET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res 39:e119.
14. International Arabidopsis Informatics Consortium. 2010. An international bioinformatics infrastructure to underpin the Arabidopsis community. Plant Cell 22:2530-2536.
15. International Health Terminology Standards Development Organisation. 2011. History of SNOMED CT. http://www.ihtsdo.org/snomed-ct/history0/. Accessed 28 Feb 2012
16. Javitt G, Katsanis S, Scott J, Hudson K. 2010. Developing the blueprint for a genetic testing registry. Public Health Genomics 13:95-105.
17. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, and others. 2007. The NCBI db Ga P database of genotypes and phenotypes. Nat Genet 39:1181-1186.
18. Mc Kusick VA. 2007. Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80:588-604.
19. Oti M, Huynen MA, Brunner HG. 2009. The biological coherence of human phenome databases. Am J Hum Genet 85:801-808.
20. Patrinos GP, Brookes AJ. 2005. DNA, diseases and databases: disastrously deficient. Trends Genet 21:333-338.
21. Robinson PN, Kohler S, Bauer S, Seelow D, Horn D, Mundlos S. 2008. The human phenotype ontology: a tool for annotating and analyzinghumanhereditary disease. Am J Hum Genet 83:610-615.
22. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, and others. 2012. Toward interoperable bioscience data. Nat Genet 44:121-126.
23. Schofield P, Rozell B, Gkoutos G. 2007. Towards a disease ontology. In: Burger A, Davidson D, Baldock R, editors. Anatomy ontologies for bioinformatics: principles and practice. London, UK: Springer Verlag. p 119-132.
24. Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM. 2010. Phenotype ontologies for mouse and man; bridging the semantic gap. Dis Models Mech 3:281-289.
25. Shublaq N. 2012a. Strategic report for translational systems biology and bioinformatics in the European Union. London, UK: INBIOMEDvision Consortium.
26. Shublaq N. 2012b. Strategic report on the re-use of clinical information for research in the European Union. London, UK: INBIOMEDvision Consortium.
27. Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, and others. 2011. Aconditional knockout resource for the genome-wide study ofmouse gene function. Nature 474:337-342.
28. Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P. 2008. Solutions for data integration in functional genomics: a critical assessment and case study. Brief Bioinform 9:532-544.
29. Smith CL, Goldsmith CA, Eppig JT. 2005. The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6:R7.
30. Swertz MA, van der Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, and others. 2010. XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol 11:R27.
31. Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ. 2009a. HGVbase G2P: a central genetic association database. Nucleic Acids Res 37(Database issue):D797-D802.
32. Thorisson GA, Muilu J, Brookes AJ. 2009b. Genotype-phenotype databases: challenges and solutions for the post-genomic era. Nat Rev Genet 10:9-18.
33. Webb AJ, Thorisson GA, Brookes AJ. 2011. An informatics project and online "knowledge centre" supporting modern genotype-to-phenotype research. Hum Mutat 32:543-550.
34. Webber C, Hehir-Kwa JY, Nguyen DQ, de Vries BB, Veltman JA, Ponting CP. 2009. Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PLo S Genet 5:e1000531.
35. World Health Organization. 2004. History of the development of the ICD. http://www.who.int/classifications/icd/en/History Of ICD. pdf. Accessed 28 Feb 2012