Databases for systems biology

Computational Systems Biology

Volumn , Issue , 2006, Pages 15-38

  Eils, Jürgen ^a   Lawerenz, Christian ^a   Astrahantseff, Kathy ^b   Ginkel, Martin ^b   Eils, Roland ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UNIVERSITY HOSPITAL ESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 45849131107     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012088786-6/50021-6     Document Type: Chapter

References (44)

1. Apweiler R., Bairoch A., Wu C., Barker W., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M., Natale D., O'Donovan C., Redaschi N., Yeh L. UniProt: The universal protein knowledge base. Nucleic Acids Res. 2004, 32:D115-D119. (Database issue).
2. Ball C., Sherlock G., Parkinson H., Rocca-Sera P., Brooksbank C., Causton H., Cavalieri D., Gaasterland T., Hingamp P., Holstege F., Ringwald M., Spellman P., Stoeckert C., Stewart J., Taylor R., Brazma A., Quackenbush J. Standards for microarray data. Science 2002, 298(5593):539.
3. Ball C., Awad I., Demeter J., Gollub J., Hebert J., Hernandez-Boussard T., Jin H., Matese J., Nitzberg M., Wymore F., Zachariah Z., Brown P., Sherlock G. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 2005, 33:D580-D582. (Database issue).
4. Barrett T., Suzek T., Troup D., Wilhite S., Ngau W.-C., Ledoux P., Rudnev D., Lash A., Fujibuchi W., Edgar R. NCBI GEO: Mining millions of expression profiles-database and tools. Nucleic Acids Res. 2005, 33:D562-D566. (Database issue).
5. Benson D., Karsch-Mizrachi I., Lipman D., Ostell J., Wheeler D. GenBank: Update. Nucleic Acids Res. 2004, 32:D23-D26. (Database issue).
6. Birney E., Andrews T., Bevan P., Caccamo M., Chen Y., Clarke L., Coates G., Cuff J., Curwen V., Cutts T., Down T., Eyras E., Fernandez-Suarez X., Gane P., Gibbins B., Gilbert J., Hammond M., Hotz H., Iyer V., Jekosch K., Kahari A., Kasprzyk A., Keefe D., Keenan S., Lehvaslaiho H., McVicker G., Melsopp C., Meidl P., Mongin E., Pettett R., Potter S., Proctor G., Rae M., Searle S., Slater G., Smedley D., Smith J., Spooner W., Stabenau A., Stalker J., Storey R., Ureta-Vidal A., Woodwark K., Cameron G., Durbin R., Cox A., Hubbard T., Clamp M. An overview of Ensembl. Genome Res. 2004, 14(5):925-928.
7. Bosak J., Bray T. XML and the second-generation web. Sci. Am. 1999, 280(5):89-93.
8. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C., Causton H., Gaasterland T., Glenisson P., Holstege F., Kim I., Markowitz V., Matese J., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29(4):365-371.
9. Brazma A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., Abeygunawardena N., Holloway E., Kapushesky M., Kemmeren P., Lara G., Oezcimen A., Rocca-Serra P., Sansone S. ArrayExpress: A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31(1):68-71.
10. Diehn M., Sherlock G., Binkley G., Jin H., Matese J., Hernandez-Boussard T., Rees C., Cherry J., Botstein D., Brown P., Alizadeh A. SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003, 31(1):219-223.
11. Discala C., Ninnin M., Achard F., Barillot E., Vaysseix G. DBcat: A catalog of biological databases. Nucleic Acids Res. 1999, 27(1):10-11.
12. Garwood K., McLaughlin T., Garwood C., Jones S., Morrison N., Taylor C., Carroll K., Evans C., Whetton A., Hart S., Stead D., Yin Z., Brown A., Hesketh A., Chater K., Hansson L., Mewissen M., Ghazal P., Howard J., Lilley K., Gaskell S., Brass A., Hubbard S., Oliver S.G., Paton N. PEDRo: A database for storing, searching, and disseminating experimental proteomics data. BMC Genomics 2004, 5(1):68.
13. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R., Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31(13):3784-3788.
14. Ginkel M., Kremling A., Nutsch T., Rehner R., Gilles E. Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 2003, 19(9):1169-1176.
15. Gollub J., Ball C., Binkley G., Demeter J., Finkelstein D., Hebert J., Hernandez-Boussard T., Jin H., Kaloper M., Matese J., Schroeder M., Brown P., Botstein D., Sherlock G. The Stanford Microarray Database: Data access and quality assessment tools. Nucleic Acids Res. 2003, 31(1):94-96.
16. Hill A., Kim H. The UAB Proteomics Database. Bioinformatics 2003, 19(16):2149-2151.
17. Hoogland C., Mostaguir K., Sanchez J., Hochstrasser D., Appel R. SWISS2DPAGE, ten years later. Proteomics 2004, 4(8):2352-2356.
18. Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T., Durbin R., Eyras E., Gilbert J., Hammond M., Huminiecki L., Kasprzyk A., Lehvaslaiho H., Lijnzaad P., Melsopp C., Mongin E., Pettett R., Pocock M., Potter S., Rust A., Schmidt E., Searle S., Slater G., Smith J., Spooner W., Stabenau A., Stalker J., Stupka E., Ureta-Vidal A., Vastrik I., Clamp M. The Ensembl genome data-base project. Nucleic Acids Res. 2002, 30(1):38-41.
19. Hucka M., Finney A., Sauro H., Bolouri H., Doyle J., Kitano H., Arkin A., Bornstein B., Bray D., Cornish-Bowden A., Cuellar A., Dronov S., Gilles E., Ginkel M., Gor V., Goryanin I., Hedley W., Hodgman T., Hofmeyr J., Hunter P., Juty N., Kasberger J., Kremling A., Kummer U., Le Novere N., Loew L., Lucio D., Mendes P., Minch E., Mjolsness E., Nakayama Y., Nelson M., Nielsen P., Sakurada T., Schaff J., Shapiro B., Shimizu T., Spence H., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531.
20. Joshi-Tope G., Gillespie M., Vastrik I., D'Eustachio P., Schmidt E., de Bono B., Jassal B., Gopinath G., Wu G., Matthews L., Lewis S., Birney E., Stein L. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res. 2005, 33:D428-D432. (Database issue).
21. Kanehisa M. A database for post-genome analysis. Trends Genet. 1997, 13(9):375-376.
22. Killion P., Sherlock G., Iyer V. The Longhorn Array Database (LAD): An open-source MIAME-compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics 2003, 4(1):32.
23. Larman C. Applying UML and Pattern 1998, Prentice-Hall, Upper Saddle River, NJ.
24. Lewis S. Gene ontology: Looking backwards and forwards. Genome Biol. 2005, 6(1):103.
25. Lloyd C., Halstead M., Nielsen P. CellML: Its future, present, and past. Prog. Biophys. Mol. Biol. 2004, 85(2/3):433-450.
26. Marinescu V., Kohane I., Riva A. The MAPPER database: A multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005, 33:D91-D97. (Database issue).
27. Mendes P. Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 1997, 22(9):361-363.
28. Nadkarni P., Brandt C. Data extraction and ad hoc query of an entity-attribute-value database. J. Am. Med. Inform. Assoc. 1998, 5(6):511-527.
29. Olivier B., Snoep J. Web-based kinetic modeling using JWS Online. Bioinformatics 2004, 20(13):2143-2144.
30. Orchard S., Hermjakob H., Apweiler R. The proteomics standards initiative. Proteomics 2003, 3(7):1374-1376.
31. Orchard S., Hermjakob H., Binz P., Hoogland C., Taylor C., Zhu W., Julian R., Apweiler R. Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics 2005, 5(2):337-339.
32. Rojas I., Bernardi L., Ratsch E., Kania R., Wittig U., Saric J. A database system for the analysis of biochemical pathways. In Silico Biol. 2002, 2(2):75-86.
33. Saal L., Troein C., Vallon-Christersson J., Gruvberger S., Borg A., Peterson C. BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data. Genome Biol. 2002, 3(8). software 0003.1-0003.6.
34. Sauro H. Jarnac: An interactive metabolic systems language. Dept. of Computer Science Technical Report No. 345 2000, 11-18. University of Herfortshire. H. Bolouri, R.C. Raymond (Eds.).
35. Schilstra M. The SBML model repository 2002, www.sbml.org/models.
36. Schomburg I., Chang A., Ebeling C., Gremse M., Heldt C., Huhn G., Schomburg D. BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res. 2004, 32:D431-D433. (Database issue).
37. Slepchenko B., Schaff J., Macara I., Loew L. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 2003, 13(11):570-576.
38. Spellman P., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M., Swiatek M., Marks W., Goncalves J., Markel S., Iordan D., Shojatalab M., Pizarro A., White J., Hubley R., Deutsch E., Senger M., Aronow B., Robinson A., Bassett D., Stoeckert C., Brazma A. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002, 3(9). research 0046.1-0046.9.
39. Swedlow J., Goldberg I., Brauner E., Sorger P. Informatics and quantitative analysis in biological imaging. Science 2003, 300(5616):100-102.
40. Takahashi K., Ishikawa N., Sadamoto Y., Sasamoto H., Ohta S., Shiozawa A., Miyoshi F., Naito Y., Nakayama Y., Tomita M. E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics 2003, 19(13):1727-1729.
41. van Helden J., Naim A., Mancuso R., Eldridge M., Wernisch L., Gilbert D., Wodak S. Representing and analyzing molecular and cellular function using the computer. Biol. Chem. 2000, 381(9/10):921-935.
42. Wheeler D., Church D., Federhen S., Lash A., Madden T., Pontius J., Schuler G., Schriml L., Sequeira E., Tatusova T., Wagner L. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 2003, 31(1):28-33.
43. Wingender E., Chen X., Fricke E., Geffers R., Hehl R., Liebich I., Krull M., Matys V., Michael H., Ohnhauser R., Pruss M., Schacherer F., Thiele S., Urbach S. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 2001, 29(1):281-283.
44. Xirasagar S., Gustafson S., Merrick B., Tomer K., Stasiewicz S., Chan D., Yost K., Yates J., Sumner S., Xiao N., Waters M. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 2004, 20(13):2004-2015.