Semantically enabling a genome-wide association study database

Journal of Biomedical Semantics

Volumn 3, Issue 1, 2012, Pages

  Beck, Tim ^a   Free, Robert C ^a   Thorisson, Gudmundur A ^a   Brookes, Anthony J ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

GWAS; Ontology; Phenotype; RDF

Indexed keywords

EID: 84911963591     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-3-9     Document Type: Article

References (70)

1. Hirschhorn JN: Genomewide association studies-illuminating biologic pathways. N Engl J Med. 2009, 360 (17): 1699-1701. 10.1056/NEJMp0808934.
2. Johnson AD, O'Donnell CJ: An open access database of genome-wide association results. BMC Med Genet. 2009, 10: 6-
3. Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ: HGVbaseG2P: a central genetic association database. Nucleic Acids Res. 2009, 37 (Database issue): D797-D802.
4. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009, 106 (23): 9362-9367. 10.1073/pnas.0903103106.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
6. Armstrong J, Bone N, Dodgson J, Beck T: The role and aims of the FYSSION project. Brief Funct Genomic Proteomic. 2007, 6 (1): 3-7. 10.1093/bfgp/elm004.
7. Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW: Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics. 2011, 12: 32-10.1186/1471-2105-12-32.
8. Beck T, Morgan H, Blake A, Wells S, Hancock JM, Mallon AM: Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics. 2009, 10 (Suppl 5): S2-10.1186/1471-2105-10-S5-S2.
9. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S, OBI Consortium: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25 (11): 1251-1255. 10.1038/nbt1346.
10. OBO Foundry Principles. http://www.obofoundry.org/crit.shtml
11. Robinson PN, Mundlos S: The human phenotype ontology. Clin Genet. 2010, 77 (6): 525-534. 10.1111/j.1399-0004.2010.01436.x.
12. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011, 39 (Web Server issue): W541-W545.
13. Medical Subject Headings. http://www.nlm.nih.gov/mesh/
14. International Classification of Diseases (ICD). http://www.who.int/classifications/icd/en/
15. Ghazvinian A, Noy NF, Musen MA: How orthogonal are the OBO Foundry ontologies?. J Biomed Semantics. 2011, 2 (Suppl 2): S2-10.1186/2041-1480-2-S2-S2.
16. Hughes LM, Bao J, Hu ZL, Honavar V, Reecy JM: Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species. J Anim Sci. 2008, 86 (6): 1485-1491. 10.2527/jas.2008-0930.
17. Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S, Papadakis K, Voight BF, Scott LJ, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers JC, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee DE, Onland-Moret NC, Bots ML, Wain LV, Elliott KS, Teumer A, Luan J, Lucas G: Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet. 2009, 41 (6): 666-676. 10.1038/ng.361.
18. Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM: Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech. 2010, 3 (5-6): 281-289.
19. Li H, Wetten S, Li L, St Jean PL, Upmanyu R, Surh L, Hosford D, Barnes MR, Briley JD, Borrie M, Coletta N, Delisle R, Dhalla D, Ehm MG, Feldman HH, Fornazzari L, Gauthier S, Goodgame N, Guzman D, Hammond S, Hollingworth P, Hsiung GY, Johnson J, Kelly DD, Keren R, Kertesz A, King KS, Lovestone S, Loy-English I, Matthews PM: Candidate single-nucleotide polymorphisms from a genomewide association study of Alzheimer disease. Arch Neurol. 2008, 65 (1): 45-53. 10.1001/archneurol.2007.3.
20. Kim H, Ramsay E, Lee H, Wahl S, Dionne RA: Genome-wide association study of acute post-surgical pain in humans. Pharmacogenomics. 2009, 10 (2): 171-179. 10.2217/14622416.10.2.171.
21. Brown SD, Hancock JM: The mouse genome. Genome Dyn. 2006, 2: 33-45.
22. Schofield PN, Hancock JM: Integration of global resources for human genetic variation and disease. Hum Mutat. 2012, 33 (5): 813-816. 10.1002/humu.22079.
23. Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, Mouse Genome Database Group: The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 2011, 39 (Database issue): D842-D848.
24. Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S, Lengger C, Maier H, Melvin D, Meziane H, Richardson D, Wells S, White J, Wood J, de Angelis MH, Brown SD, Hancock JM, Mallon AM, EUMODIC Consortium: EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res. 2010, 38 (Database issue): D577-D585.
25. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA: Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012, 13 (1): R5-10.1186/gb-2012-13-1-r5.
26. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biol. 2010, 11 (1): R2-10.1186/gb-2010-11-1-r2.
27. Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN: Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome. 2009, 20 (8): 457-461. 10.1007/s00335-009-9208-3.
28. Linked Data - Connect Distributed Data across the Web. http://linkeddata.org
29. Wilkinson MD, Vandervalk B, McCarthy L: The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. J Biomed Semantics. 2011, 2 (1): 8-10.1186/2041-1480-2-8.
30. Zappa A, Splendiani A, Romano P: Towards linked open gene mutations data. BMC Bioinformatics. 2012, 13 (Suppl 4): S7-10.1186/1471-2105-13-S4-S7.
31. Laurila JB, Naderi N, Witte R, Riazanov A, Kouznetsov A, Baker CJ: Algorithms and semantic infrastructure for mutation impact extraction and grounding. BMC Genomics. 2010, 11 (Suppl 4): S24-10.1186/1471-2164-11-S4-S24.
32. Riazanov A, Laurila JB, Baker CJ: Deploying mutation impact text-mining software with the SADI Semantic Web Services framework. BMC Bioinformatics. 2011, 12 (Suppl 4): S6-10.1186/1471-2105-12-S4-S6.
33. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008, 41 (5): 706-716. 10.1016/j.jbi.2008.03.004.
34. UniProt Consortium: Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40 (Database issue): D71-D75.
35. Groth P, Gibson A, Velterop J: The anatomy of a nanopublication. Information Services and Use. 2010, 30 (1): 51-56.
36. Giardine B, Borg J, Higgs DR, Peterson KR, Philipsen S, Maglott D, Singleton BK, Anstee DJ, Basak AN, Clark B, Costa FC, Faustino P, Fedosyuk H, Felice AE, Francina A, Galanello R, Gallivan MV, Georgitsi M, Gibbons RJ, Giordano PC, Harteveld CL, Hoyer JD, Jarvis M, Joly P, Kanavakis E, Kollia P, Menzel S, Miller W, Moradkhani K, Old J: Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet. 2011, 43 (4): 295-301. 10.1038/ng.785.
37. nanopub: a beginner's guide to data publishing. http://www.nanopub.org/
38. Thorisson GA: Accreditation and attribution in data sharing. Nat Biotechnol. 2009, 27 (11): 984-985.
39. SNOMED CT. http://www.ihtsdo.org/snomed-ct/
40. Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL: Annotating the human genome with Disease Ontology. BMC Genomics. 2009, 10 (Suppl 1): S6-10.1186/1471-2164-10-S1-S6.
41. PubMed Help. http://www.ncbi.nlm.nih.gov/books/NBK3827
42. Robinson PN, Kohler S, Bauer S, Seelow D, Horn D, Mundlos S: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet. 2008, 83 (5): 610-615. 10.1016/j.ajhg.2008.09.017.
43. Tracker: Human Phenotype Requests. http://sourceforge.net/tracker/?group_id=76834&atid=1112722
44. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN: Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc. 2009, 2009: 7069-7072.
45. Amberger J, Bocchini CA, Scott AF, Hamosh A: McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009, 37 (Database issue): D793-D796.
46. Smith CL, Goldsmith CA, Eppig JT: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2005, 6 (1): R7-
47. Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D: myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010, 38 (Web Server issue): W677-W682.
48. OMIM. Bromodomain Adjacent to Zinc Finger Domain, 1B; BAZ1B. http://omim.org/entry/605681
49. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006, 34 (Web Server issue): W729-W732.
50. Gates H, Mallon AM, Brown SD, EUMODIC Consortium: High-throughput mouse phenotyping. Methods. 2011, 53 (4): 394-404. 10.1016/j.ymeth.2010.12.017.
51. The Open PHACTS Nanopublication Guidelines. http://www.nanopub.org/guidelines/current
52. de Lusignan S, Chan T, Jones S: Large complex terminologies: more coding choice, but harder to find data-reflections on introduction of SNOMED CT (Systematized Nomenclature of Medicine-Clinical Terms) as an NHS standard. Inform Prim Care. 2011, 19 (1): 3-5.
53. Trieschnigg D, Pezik P, Lee V, de Jong F, Kraaij W, Rebholz-Schuhmann D: MeSH Up: effective MeSH text classification for improved document retrieval. Bioinformatics. 2009, 25 (11): 1412-1418. 10.1093/bioinformatics/btp249.
54. Jonquet C, Shah NH, Musen MA: The open biomedical annotator. Summit on Translat Bioinforma. 2009, 2009: 56-60.
55. Aronson AR: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp. 2001, 2001: 17-21.
56. Palleja A, Horn H, Eliasson S, Jensen LJ: DistiLD Database: diseases and traits in linkage disequilibrium blocks. Nucleic Acids Res. 2012, 40 (Database issue): D1036-D1040.
57. Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J: GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2012, 40 (Database issue): D1047-D1054.
58. Sardana D, Vasa S, Vepachedu N, Chen J, Gudivada RC, Aronow BJ, Jegga AG: PhenoHM: human-mouse comparative phenome-genome server. Nucleic Acids Res. 2010, 38 (Web Server issue): W165-W174.
59. Tim Berners-Lee: Linked Data - Design Issues. http://www.w3.org/DesignIssues/LinkedData.html
60. The D2RQ Platform. http://d2rq.org/
61. Triplify. http://triplify.org/Overview
62. BioPortal REST services. http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
63. Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics. 2010, 11 (Suppl 12): S12-10.1186/1471-2105-11-S12-S12.
64. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010, 38 (Database issue): D5-D16.
65. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A: BioMart-biological queries made easy. BMC Genomics. 2009, 10: 22-10.1186/1471-2164-10-22.
66. Apache Jena TDB. http://incubator.apache.org/jena/documentation/tdb/index.html
67. Fuseki: serving RDF data over HTTP. http://incubator.apache.org/jena/documentation/serving_data/index.html
68. Bizer C, Lehmann J, Kobilarov G, Auer S, Becker C, Cyganiak R, Hellmann S: DBpedia - A Crystallization Point for the Web of Data. Journal of Web Semantics: Science, Services and Agents on the World Wide Web. 2009, 7: 154-10.1016/j.websem.2009.07.002.
69. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium: Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010, 1 (Suppl 1): S7-10.1186/2041-1480-1-S1-S7.
70. PRO, the Publishing Roles Ontology. http://purl.org/spar/pro/Role