Microbial genome data resources

Current Opinion in Biotechnology

Volumn 18, Issue 3, 2007, Pages 267-272

  Markowitz, Victor M ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA PROCESSING; ENERGY RESOURCES; ENVIRONMENTAL PROTECTION; HEALTH CARE; MICROBIOLOGY;

AGGREGATE GENOMES; ALTERNATIVE ENERGY; MICROBIAL COMMUNITIES; MICROBIAL GENOME;

GENES;

CLEANING; ENERGY YIELD; ENVIRONMENT; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; HEALTH CARE; INFORMATION PROCESSING; LIFE CYCLE; MICROBIAL GENETICS; MICROFLORA; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; SCIENTIST;

ENVIRONMENTAL REMEDIATION; GENOME, BACTERIAL;

EID: 34249943969     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2007.04.005     Document Type: Review

References (58)

1. Liolios K., Tavernarakis N., Hugenholtz P., and Kyrpides N.C. The genomes on line database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 34 (2006) D332-D334
2. th International Conference on Very Large Databases, Toronto, Canada, August 31-September 3 2004. Editors: Nascimento MA, Ozsu MT, Kossman D, Miller RJ, Blakeley JA, Schiefer KB; Morgan Kaufmann. pp. 1198-1201.
3. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., Giegerich R., and Pühler A. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31 (2003) 2187-2195
4. Hauser L., Larimer F., Land M., Shah M., and Uberbacher E. Analysis and annotation of microbial genome sequences. Genet Eng (NY) 26 (2004) 225-238
5. Tatusov R.L., Koonin E.V., and Lipman D.J. A genomic perspective on protein families. Science 278 (1997) 631-637
6. Kanehisa M., Goto S., Kawashima S., Okuno Y., and Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 32 (2004) D277-D280
7. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., et al. The Pfam protein families database. Nucleic Acids Res 32 (2004) D138-D141
8. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., et al. New developments in the InterPro database. Nucleic Acids Res 35 (2007) D224-D228
9. Chen K., and Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1 (2005) 106-112. The authors review the key challenges in the processing and analysis of microbial community sequence data, including assembly, gene prediction, and classification (binning) methods for such data.
10. Bowers P.M., Pellegrini M., Thompson M.J., Fierro J., Yeates T.O., and Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 5 (2004) R35
11. Benson D.A., Karsch-Mizrahi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucleic Acids Res 35 (2007) D21-D25
12. Kulikova T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya, Bower L., Browne P., et al. EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35 (2007) D16-D20
13. Sugawara H., Abe T., Gojobori T., and Tateno Y. DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res 35 (2007) D13-D15
14. Pruitt K.D., Tatusova T., and Maglott D.R. NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts, and proteins. Nucleic Acids Res 35 (2007) D61-D65
15. Kersey P., Bower L., Morris L., Horne A., Petryszak R., Kanz C., Kanapin A., Das U., Michoud K., Phan I., et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteoms. Nucleic Acids Res 33 (2005) D297-D302
16. Maglott D., Ostell J., Pruitt K.D., and Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35 (2007) D26-D31
17. Schneider K.L., Pollard K.S., Baertsch R., Pohl A., and Lowe T.M. The UCSC archaeal genome browser. Nucleic Acids Res 34 (2006) D407-D410
18. Peterson J.D., Umayam L.A., Dickinson T., Hickey E.K., and White O. The comprehensive microbial resource. Nucleic Acids Res 29 (2001) 123-125
19. Overbeek R., Larsen N., Walunas T., D'Souza M., Pusch G., Selkov E., Liolios K., Joukov V., Kaznadzey D., Anderson I., et al. The ERGO genome analysis and discovery system. Nucleic Acids Res 31 (2003) 164-171
20. Alm E.J., Huang K.H., Price M.N., Koche R.P., Keller K., Dubchak I.L., and Arkin A.P. The Microbes Online web site for comparative genomics. Genome Res 15 (2005) 1015-1022. One of the existing integrated microbial genome resources described in more detail than other similar resources.
21. Maltsev N., Glass E., Sulakhe D., Rodriguez A., Syed M.H., Bompada T., Zhang Y., and D'Souza M.D. PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res 34 (2006) D369-D372
22. Markowitz V.M., Korzeniewski F., Palaniappan K., Szeto E., Werner G., Padki A., Zhao X., Dubchak I., Hugenholtz P., Anderson I., et al. The Integrated Microbial Genomes (IMG) system. Nucleic Acids Res 34 (2006) D344-D348
23. Uchiyama I. MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res 35 (2007) D343-D346
24. Haft D.H., Selengut J.D., Brinkac L.M., Zafar N., and White O. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21 (2005) 293-306. Representative of efforts to enhance functional characterization of microbial genomes in terms of various metrics, such as gene content, presence of metabolic pathways, and various phenotypic properties.
25. D'Ascenzo M.D., Collmer A., and Martin G.B. PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucleic Acids Res 32 (2004) 3124-3135
26. Winsor G.L., Lo R., Ho Sui S.J., Ung K.S.E., Huang S., Cheng D., Ho Ching W.K., Hancock R.E.W., and Brinkman F.S.L. Pseudomonas aeruginosa genome database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 33 (2005) D338-D343
27. Glasner J.D., Rusch M., Liss P., Plunkett G., Cabot E.L., Darling A., Bradley D.A., Infield-Harm P., Gilson M.C., and Perna N.T. ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res 34 (2006) D41-D45
28. Gene Ontology Consortium. The Gene Ontology database and informatics resource. Nucleic Acids Res 32 (2004) 258-261
29. Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R., et al. The subsystems aproach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33 (2005) 5691-5702. A decentralized model of annotation, whereby biological process specific subsystems are annotated jointly across collections of available genomes, is discussed and illustrated using several subsystems.
30. Myhre S., Tveit H., Mollestad T., and Laegreid A. Additional gene ontology structure for improved biological reasoning. Bioinformatics 22 (2006) 2020-2027
31. Deutschbauer A.M., Chivian D., and Arkin A.P. Genomics for environmental microbiology. Curr Opin Biotechnol 17 (2006) 229-235. Overview of the emerging field of metagenomics.
32. Tringe S.G., von Mering C., Kobayashi A., Salamov A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., et al. Comparative metagenomics of microbial communities. Science 308 (2005) 554-557. Introduces the concept of environmental gene tag (EGT) analysis to cope with the fragmentation and incompleteness of microbial community sequences. Variants of EGT analysis have been used extensively in metagenome studies.
33. DeLong E.F., Preston C.M., Mincer T., Rich V., Hallam S.J., Frigaard N.U., Martinez A., Sullivan M.B., Edwards R., Brito B.R., et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311 (2006) 1355-1359
34. Markowitz V.M., Ivanova N.N., Palaniappan K., Szeto E., Korzeniewski F., Lykidis A., Anderson I., Mavrommatis K., Kunin V., Garcia Martin H., et al. An experimental metagenome data management and analysis system. Bioinformatics 22 (2006) e359-e367
35. Lombardot T., Kottmann R., Pfeffer H., Richter M., Teeling H., Quast C., and Glockner F.O. Megx.net - database resources for marine ecological genomics. Nucleic Acids Res 34 (2006) D390-D393
36. Shah SP, Huang Y, Xu T, Yuen MMS, Ling J, Ouellette BFF: Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics 2005, 6:10.11861/1471-2105-6-34. http://www.biomedcentral.com/1471-2105/6/34/.
37. Kasprzyk A., Keefe D., Smedley D., London D., Spooner W., Melsopp C., Hammond M., Rocca-Serra P., Cox T., and Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14 (2004) 160-169
38. Lee TJ, Pouliot Y, Wagner V, Gupta P, Stringer-Calvert DWJ, Tenenbaum JD, Karp PD: BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics 2006, 7:10.1186/1471-2105-7-170. http://www.biomedcentral.com/1471-2105/7/170.
39. Searls D.B. Data integration: challenges for drug discovery. Nat Rev Drug Discov 4 (2005) 45-58. A comprehensive review of biological data integration problems from a domain application (rather than information technology) perspective. Covers diverse aspects of integration for data generated directly by technology platforms through data derived although various transformations.
40. Wong L. Technologies for integrating biological data. Brief Bioinform 3 (2002) 389-404
41. Stein L.D. Integrating biological databases. Nat Rev Genet 4 (2003) 337-345
42. Hernandez T., and Kambhampati S. Integration of biological sources: current systems and challenges ahead. SIGMOD Record 33 (2004) 51-60
43. In: Lacroix Z., and Critchlow T. (Eds). Bioinformatics: Managing Scientific Data (2003), Morgan Kaufman Publishers
44. Halevy A.Y., Ashish N., Bitton D., Carey M.J., Draper D., Pollock J., Rosenthal A., and Sikka V. Enterprise information integration: successes, challenges and controversies. In: Ozcan F. (Ed). Proceedings of the ACM SIGMOD International Conference on Management of Data. Maryland, USA, June 14-16, 2005 (2005), ACM 778-787. A collection of short articles that illustrate the complexity of data integration in general, and in particular the overwhelming importance of application-specific semantics of data in integration.
45. Halevy A.Y. Why your data won't mix: semantic heterogeneity. ACM Queue 3 (2005) 50-58. This paper discusses the crucial role of semantic heterogeneity in data integration and shows how leveraging past experience could facilitate addressing this problem, thus making a strong case for data and tool sharing.
46. Cohen S, Cohen-Boulakia S, Davidson S: Towards a model of provenance and user views in scientific workflows. In Data Integration in the Life Sciences, Third International Workshop, DILS 2006, Hinxton, UK, July 20-2, 2006, Proceedings. Lecture Notes in Computer Science 4075. Editors: Leser U, Naumann F, Eckman BA; Springer. pp. 264-279.
47. Buneman P., Chapman A., and Cheney J. Provenance Management in Curated Databases. In: Chaudhuri S., Hristidis V., and Polyzotis N. (Eds). Proceedings of ACM SIGMOD International Conference on Management of Data. Chicago, Illinois, USA, June 27-9, 2006 (2006), ACM 539-550. The authors discuss data provenance for curated biological databases and proposes a practical approach for tracking provenance.
48. Simmhan Y.L., Plale B., and Gannon D. A survey of data provenance in e-science. SIGMOD Record 34 (2005) 31-36
49. Gray J., Liu D.T., Nieto-Santisteban M., Szalay A., DeWitt D.J., and Heber G. Scientific data management in the coming decade. SIGMOD Record 34 (2005) 34-41. Discusses the challenges of large-scale scientific data management and the technical areas that are critical to address them.
50. Galperin M.Y. The molecular biology database collection: 2007 update. Nucleic Acids Res 35 (2007) D3-D4
51. Jagadish H.V., and Olken F. Database management for life science research. SIGMOD Record 33 (2004) 15-20
52. Franklin M., Halevy A.Y., and Maier D. From databases to dataspaces: a new abstraction for information management. SIGMOD Record 34 (2005) 27-33
53. Overbeek R., Larsen N., Smith W., Maltsev N., and Selkov E. Representation of function: the next step. Gene 191 (1997) GC1-GC9
54. Overbeek R., Larsen N., Pusch G., D'Souza M.D., Selkov Jr. E., Kyrpides N.C., Fonstein M., Maltsev N., and Selkov E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res 28 (2000) 123-125
55. Cohen-Boulakia S., Davidson S., Froidevaux C., Lacroix Z., and Vidal M.E. Path-based systems to guide scientists in the maze of biological data sources. J Bioinform Comput Biol 4 (2006) 1069-1095
56. No authors listed. Sustainable databases. Nat Cell Biol 8 (2006) 1311. A compelling discussion of the problems facing biological data resources and their uncertain future.
57. No authors listed. The database revolution. Nature 445 (2007) 229-230
58. Committee on Metagenomics. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (2007), National Academies Press. http://www.nap.edu