Standardizing the standards

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Quackenbush, John ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CELL FUNCTION; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA EXTRACTION; DATA SYNTHESIS; DNA MICROARRAY; DNA SEQUENCE; METABOLOMICS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; SHORT SURVEY; STANDARD; STANDARDIZATION; SYSTEMS BIOLOGY;

BIOMETRY; COMPUTATIONAL BIOLOGY; MICROARRAY ANALYSIS; REFERENCE STANDARDS;

EID: 33745476107     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100052     Document Type: Short Survey

References (15)

1. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N (2004) Submission of microarray data to public repositories. PLoS Biol 2: E317
2. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert Jr CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J (2002) The underlying principles of scientific publication. Bioinformatics 18: 1409
3. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet 29: 365-371
4. Finney A, Hucka M (2003) Systems biology markup language: level 2 and beyond. Biochem Soc Trans 31: 1472-1473
5. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R (2004) The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 22: 177-183
6. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531
7. Keller A, Eng J, Zhang N, Li X-j, Aebersold R (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol doi:10.1038/msb4100024
8. Lindon JC, Nicholson JK, Holmes E, Keun HC, Craig A, Pearce JT, Bruce SJ, Hardy N, Sansone SA, Antti H, Jonsson P, Daykin C, Navarange M, Beger RD, Verheij ER, Amberg A, Baunsgaard D, Cantor GH, Lehman-McKeeman L, Earll M, Wold S, Johansson E, Haselden JN, Kramer K, Thomas C, Lindberg J, Schuppe-Koistinen I, Wilson ID, Reily MD, Robertson DG, Senn H, Krotzky A, Kochhar S, Powell J, van der Ouderaa F, Plumb R, Schaefer H, Spraul M (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23: 833-838
9. Lloyd CM, Halstead MD, Nielsen PF (2004) CellML: it's future, present and past. Prog Biophys Mol Biol 85: 433-450
10. Orchard S, Hermjakob H, Julian Jr RK, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R (2004) Common interchange standards for proteomics data: public availability of tools and schema. Proteomics 4: 490-491
11. Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22: 1459-1466
12. Sansone S, Morrison N, Rocca-Serra P, Fostel J (2005) Standardization initiatives in the (eco)toxicogenomics domain: a review. Comp Funct Genomics 8: 633-641
13. Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert Jr CJ, Brazma A (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 3 RESEARCH0046
14. Stanislaus R, Jiang LH, Swartz M, Arthur J, Almeida JS (2004) An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinform 5: 9
15. Wang X, Gorlitsky R, Almeida JS (2005) From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nat Biotechnol 23: 1099-1103