IntegromeDB: An integrated system and biological search engine

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Baitaluk, Michael ^a   Kozhenkov, Sergey ^a   Dubinina, Yulia ^a   Ponomarenko, Julia ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Biological ontologies; Data integration; Search engine

Indexed keywords

ARTICLE; COMPUTER INTERFACE; CONTENT ANALYSIS; DATA ANALYSIS; GENE CONTROL; GENE EXPRESSION; GENETIC DATABASE; METAGENOMICS; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; SEARCH ENGINE; WEB BROWSER; BIOLOGY; COMPUTER PROGRAM; FACTUAL DATABASE; GENETICS; INTERNET; METHODOLOGY; PROTEIN ANALYSIS;

PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENE EXPRESSION; INTERNET; METAGENOMICS; PROTEIN INTERACTION MAPPING; PROTEINS; SEARCH ENGINE; SOFTWARE;

EID: 84855894674     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-35     Document Type: Article

References (34)

1. Wu C, Bairoch A, Apweiler R, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006, 34:D187-191. 10.1093/nar/gkj161, 1347523, 16381842.
2. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2011, 39:32-7.
3. Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D. GeneCards Version 3: the human gene integrator. Database 2010, doi: 10.1093/database/baq020.
4. Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, . RGD Team The Rat Genome Database, update 2007 - easing the path from disease to data and back again. Nucleic Acids Res 2007, 35:658-62. RGD Team.
5. Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, . the Mouse Genome Database Group The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 2011, 39(suppl 1):842-848. the Mouse Genome Database Group.
6. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009, 10(11):R130. 10.1186/gb-2009-10-11-r130, 3091323, 19919682.
7. Köhler J, et al. Graph-based analysis and visualization of experimental results with Ondex. Bioinformatics 2006, 22(11):1383-1390. 10.1093/bioinformatics/btl081, 16533819.
8. Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME. Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics 2008, 6(3):205-17. 10.1007/s12021-008-9033-y, 2689790, 18958629.
9. Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34:D504-6. 10.1093/nar/gkj126, 1347488, 16381921.
10. Blake A, Pickford K, Greenaway S, Thomas S, Pickard A, Williamson CM, Adams NC, Walling A, Beck T, Fray M, Peters J, Weaver T, Brown SD, Hancock JM, Mallon AM. MouseBook: an integrated portal of mouse resources. Nucleic Acids Res 2010, 38:D593-9. 10.1093/nar/gkp867, 2808969, 19854936.
11. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucl Acids Res 2011, 39:D52-D57. 10.1093/nar/gkq1237, 3013746, 21115458.
12. Galperin MY, Cochrane GR. The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res 2011, 39:D1-6. 10.1093/nar/gkq1243, 3013748, 21177655.
13. Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M. BiologicalNetworks 2.0--an integrative view of genome biology data. BMC Bioinformatics 2010, 11:610. 10.1186/1471-2105-11-610, 3019228, 21190573.
14. Baitaluk M, Ponomarenko J. Semantic Integration of Data on Transcriptional Regulation. Bioinformatics 2010, 26(13):1651-1661. 10.1093/bioinformatics/btq231, 2887046, 20427517.
15. Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M. BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies. BMC Syst Biol 2011, 5:7. 10.1186/1752-0509-5-7, 3027118, 21235794.
16. RDF. , http://www.w3.org/RDF/
17. Good BM, Wilkinson MD. The Life Sciences Semantic Web is full of creeps!. Brief Bioinform 2006, 7:275-286. 10.1093/bib/bbl025, 16899496.
18. Wright A. Searching the Deep Web. CACM 2008, 51(10):14-15.
19. Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH. An overview of the PubChemBioAssay resource. Nucleic Acids Res 2010, 38:D255-66. 10.1093/nar/gkp965, 2808922, 19933261.
20. Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2011. Nucleic Acids Res 2011, 39:D519-9.
21. Hubbard TJP, et al. Ensembl 2007. Nucleic Acids Res 2007, 35:D610-D617. 10.1093/nar/gkl996, 1761443, 17148474.
22. Apache Lucene project. , http://lucene.apache.org
23. Page L, Brin S, Motwani R, Winograd T. The PageRank citation ranking: Bringing order to the Web. 1999,
24. Levenshtein VI. Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady 1966, 10:707-10.
25. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360. 10.1093/nar/gkp896, 2808910, 19880382.
26. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: The Pathway Interaction Database. Nucleic Acids Res 2009, 37:D674-9. 10.1093/nar/gkn653, 2686461, 18832364.
27. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of biological pathways and processes. Nucleic Acids Res 2009, 37:D619-22. 10.1093/nar/gkn863, 2686536, 18981052.
28. Biocarta pathways. , http://www.biocarta.com
29. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A. NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res 2011, 39:D1005-10. 10.1093/nar/gkq1184, 3013736, 21097893.
30. Parkinson, et al. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucl Acids Res 2009, 37:D868-72. 10.1093/nar/gkn889, 2686529, 19015125.
31. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157. 10.1093/nar/gkq1027, 3013655, 21037258.
32. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36:D149-53. 2238905, 18158296.
33. Protein Data Bank (PDB). , http://www.rcsb.org
34. Wikipedia. , http://www.wikipedia.org