Towards linked open gene mutations data

BMC Bioinformatics

Volumn 13, Issue SUPPL.4, 2012, Pages

  Zappa, Achille ^a,b   Splendiani, Andrea ^c,d   Romano, Paolo ^a  

^a UNIVERSITY OF GENOA   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

^c ROTHAMSTED RESEARCH   (United Kingdom)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AS-LINKS; AUTOMATIC MAPPING; BIBLIOGRAPHIC REFERENCES; BIOLOGICAL DATABASE; CORRELATION ANALYSIS; DATA RETRIEVAL; DEDICATED SYSTEMS; EXTERNAL SYSTEMS; GENE MUTATIONS; HIGH-THROUGHPUT TECHNOLOGIES; LINKED DATUM; LINKED OPEN DATUM; PERSONALIZED MEDICINES; QUERY PERFORMANCE; RDF GRAPH; RELATIONAL DATABASE; SOMATIC MUTATION; SPARQL QUERIES; TEST SETS; TP53 MUTATION;

BIBLIOGRAPHIC RETRIEVAL SYSTEMS; DATABASE SYSTEMS; GENES;

DATA INTEGRATION;

ARTICLE; COMPUTER PROGRAM; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; INTERNET; MUTATION; SEMANTICS; TUMOR SUPPRESSOR GENE;

DATABASES, GENETIC; GENES, P53; GENETIC VARIATION; HUMANS; INTERNET; MUTATION; SEMANTICS; SOFTWARE;

EID: 84864940723     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S4-S7     Document Type: Article

References (52)

1. Berners-Lee T, Hendler J, Lassila O. The semantic web. Scientific American 2001, 34-43.
2. Stephens S, LaVigna D, DiLascio M, Luciano J. Aggregation of bioinformatics data using Semantic Web technology. Journal of Web Semantics 2006, 4:216-221.
3. Dhanapalan L, Chen JY. A case study of integrating protein interaction data using semantic web technology. Int J Bioinform Res Appl 2007, 3:286-302. 10.1504/IJBRA.2007.015004, 18048193.
4. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web. BMC Bioinformatics 2007, 8(Suppl 3):S2. 10.1186/1471-2105-8-S3-S2, 1892099, 17493285.
5. Deus HF, Stanislaus R, Veiga DF, Behrens C, Wistuba II, Minna JD, Garner HR, Swisher SG, Roth JA, Correa AM, Broom B, Coombes K, Chang A, Vogel LH, Almeida JS. A Semantic Web management model for integrative biomedical informatics. PLoS One 2008, 3:e2946. 10.1371/journal.pone.0002946, 2491554, 18698353.
6. Miles A, Zhao J, Klyne G, White-Cooper H, Shotton D. OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster. J Biomed Inform 2010, 43:752-761. 10.1016/j.jbi.2010.04.004, 20382263.
7. Bizer C, Heath T, Berners-Lee T. Linked Data-The Story So Far. International Journal on Semantic Web and Information Systems 2009, 5:1-22.
8. RDF-Semantic Web Standards. , http://www.w3.org/RDF/
9. RdfAndSql-W3C Wiki. , http://www.w3.org/wiki/RdfAndSql
10. Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J. Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics 2008, 41:706-716. 10.1016/j.jbi.2008.03.004, 18472304.
11. SPARQL Query Language for RDF. , http://www.w3.org/TR/rdf-sparql-query/
12. Linked Data-Connect Distributed Data across the Web. , http://linkeddata.org/
13. The Linking Open Data cloud diagram. , http://lod-cloud.net/
14. The 1000 Genomes Consortium A map of human genome variation from population scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Consortium.
15. 1000 Genomes. , http://www.1000genomes.org/
16. Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. Bioinformatics challenges for personalized medicine. Bioinformatics 2011, 27:1741-1748. 10.1093/bioinformatics/btr295, 3117361, 21596790.
17. Cooper DN, Chen J-M, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010, 31:631-655. 10.1002/humu.21260, 20506564.
18. Laurila JB, Naderi N, Witte R, Riazanov A, Kouznetsov A, Baker CJO. Algorithms and semantic infrastructure for mutation impact extraction and grounding. BMC Genomics 2010, 11(Suppl 4):S24. 10.1186/1471-2164-11-S4-S24, 3005927, 21143808.
19. Human Genome Variation Society. , http://www.hgvs.org/
20. Human Genome Variation Society database list. , http://www.hgvs.org/dblist/dblist.html
21. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 2011, 32:557-563. 10.1002/humu.21438, 21520333.
22. Human Variome Project. , http://www.humanvariomeproject.org/
23. den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot CC, Hardison RC, Povey S, Cotton RG. Sharing data between LSDBs and central repositories. Hum Mutat 2009, 30:493-495. 10.1002/humu.20977, 19306393.
24. VariO. , http://www.variationontology.org
25. Mutation Impact Ontology-OWL format. , http://unbsj.biordf.net/ontologies/mutation-impact-ontology.owl
26. Wilkinson MD, McCarthy L, Vandervalk B, Withers D, Kawas E, Samadian S. SADI, SHARE, and the in silico scientific method. BMC Bioinformatics 2010, 11(Suppl 12):S7. 10.1186/1471-2105-11-S12-S7, 3040533, 21210986.
27. Riazanov A, Laurila JB, Baker CJO. 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, 3194198, 21992079.
28. Bada M, Eilbeck K. Toward a richer representation of sequence variation in the Sequence Ontology. Annotation, Interpretation and Management of Mutations 2010 Ghent, Belgium, Baker CJO, Witte R, Rebholz-Schuhmann D, Proceedings of the ECCB 2010 Workshop: Annotation, Interpretation and Management of Mutations (AIMM-2010), Ghent, Belgium, September 26, 2010, CEUR Workshop Proceedings, ISSN 1613-0073, online: http://CEUR-WS.org/Vol-645/.
29. D2RQ-Treating Non-RDF Databases as Virtual RDF Graphs-Chris Bizer. , http://www4.wiwiss.fu-berlin.de/bizer/d2rq/index.htm
30. TDB-A SPARQL Database for Jena. , http://jena.sourceforge.net/TDB/
31. Jena Semantic Web Framework. , http://openjena.org/index.html
32. Joseki-A SPARQL Server for Jena. , http://joseki.sourceforge.net/
33. Pubby-A Linked Data Frontend for SPARQL Endpoints. , http://www4.wiwiss.fu-berlin.de/pubby/
34. IARC TP53 DATABASE. , http://www-p53.iarc.fr/
35. Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P, Olivier M. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat 2007, 28:622-629. 10.1002/humu.20495, 17311302.
36. Marra D, Romano P. Integrating mutation data of the TP53 human gene in the bioinformatics network environment. Proceedings of the First International Conference on Bioinformatics Research and Development BIRD '07: 12-14 March 2007; Berlin 2007, 453-463. Springer Verlag Berlin Heidelberg, Springer Lecture Notes in Bioinformatics LNBI 4414.
37. SRS at the National Cancer Research Institute in Genova. , http://bioinformatics.istge.it/srs71/
38. Sioutos N, de Coronado S, Haber MW, Hartel FW, Shaiud W-L, Wright LW. NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics 2007, 40:30-43. 10.1016/j.jbi.2006.02.013, 16697710.
39. NCI Thesaurus. , http://ncit.nci.nih.gov/
40. Welcome to the Bibliographic Ontology Website | The Bibliographic Ontology. , http://bibliontology.com/
41. BibTeX Ontology. , http://data.bibbase.org/ontology/
42. Goh K-I, Cusick ME, Valle D, Childs B, Vidal M, Barabási A-L. The Human Disease Network. Proc Natl Acad Sci USA 2007, 104:8685-8690. 10.1073/pnas.0701361104, 1885563, 17502601.
43. Diseasome: explore the human disease network. , http://diseasome.eu/
44. dbpedia.org: About. , http://www.dbpedia.org/
45. HUGO Gene Nomenclature Committee Home Page. , http://www.genenames.org/
46. Linked Life Data-A Semantic Data Integration Platform for the Biomedical Domain. , http://linkedlifedata.com/
47. Heath T, Bizer C. Linked Data: Evolving the Web into a Global Data Space 2011, Morgan & Claypool, [Hendler J, van Harmelen F (Series Editor) Synthesis Lectures on the Semantic Web: Theory and Technology, 1:1].
48. Marbles Linked Data Engine. , http://marbles.sourceforge.net/
49. Heim P, Hellmann S, Lehmann J, Lohmann S, Stegemann T. RelFinder: Revealing Relationships in RDF Knowledge Bases. Semantic Multimedia: Proceedings of the 4th International Conference on Semantic and Digital Media Technologies, SAMT 2009 Graz, Austria, December 2-4, 2009 182-187. Chua T-S, Kompatsiaris Y, Mérialdo B, Haas W, Lecture Notes in Computer Science LNCS 5887 (Jan 13, 2010) ISBN 978-3642105425.
50. TP53/IARC LOGVD SPARQLer-An RDF Query Server-National Cancer Research Institute, Genova, Italy. , http://bioinformatics.istge.it/logvdsparql/
51. TP53/IARC LOGVD Pubby-National Cancer Research Institute, Genova, Italy. , http://bioinformatics.istge.it/logvd/
52. Vidal M. A biological atlas of functional maps. Cell 2001, 104(3):333-9. 10.1016/S0092-8674(01)00221-5, 11239391.