Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database -Xindice

详细信息    查看全文

• 作者：Feng Li (1) (2)
  Maoyu Li (1)
  Zhiqiang Xiao (1)
  Pengfei Zhang (1)
  Jianling Li (1)
  Zhuchu Chen (1) (2)
  
• 刊名：BMC Bioinformatics
• 出版年：2006
• 出版时间：December 2006
• 年：2006
• 卷：7
• 期：1
• 全文大小：3292KB
• 参考文献：1. Tyers M, Mann M: From genomics to proteomics. / Nature 2003,422(6928):193-97. CrossRef
  2. Bogyo M, Hurley JH: Proteomics and genomics. / Curr Opin Chem Biol 2003,7(1):2-. CrossRef
  3. Williams M: Genomics, proteomics and gnomics. / Curr Opin Investig Drugs 2001,2(4):437-39.
  4. Binz PA, Muller M, Walther D, Bienvenut WV, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins MR, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD, Hochstrasser DF: A molecular scanner to automate proteomic research and to display proteome images. / Anal Chem 1999,71(21):4981-988. CrossRef
  5. Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM: The need for a public proteomics repository. / Nat Biotechnol 2004,22(4):471-72. CrossRef
  6. Orchard S, Hermjakob H, Julian RKJ, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R: Common interchange standards for proteomics data: Public availability of tools and schema. / Proteomics 2004,4(2):490-91. CrossRef
  7. Laoudj-Chenivesse D, Marin P, Bennes R, Tronel-Peyroz E, Leterrier F: High performance two-dimensional gel electrophoresis using a wetting agent Tergitol NP7. / Proteomics 2002,2(5):481-85. CrossRef
  8. Jones A, Hunt E, Wastling JM, Pizarro A, Stoeckert CJJ: An object model and database for functional genomics. / Bioinformatics 2004,20(10):1583-590. CrossRef
  9. Garwood KL, Taylor CF, Runte KJ, Brass A, Oliver SG, Paton NW: Pedro: a configurable data entry tool for XML. / Bioinformatics 2004,20(15):2463-465. CrossRef
  10. Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJ, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW: PEDRo: a database for storing, searching and disseminating experimental proteomics data. / BMC Genomics 2004,5(1):68. CrossRef
  11. Stanislaus R, Jiang LH, Swartz M, Arthur J, Almeida JS: An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. / BMC Bioinformatics 2004, 5:9. CrossRef
  12. 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: A common open representation of mass spectrometry data and its application to proteomics research. / Nat Biotechnol 2004,22(11):1459-466. CrossRef
  13. Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG: A systematic approach to modeling, capturing, and disseminating proteomics experimental data. / Nat Biotechnol 2003,21(3):247-54. CrossRef
  14. Achard F, Vaysseix G, Barillot E: XML, bioinformatics and data integration. / Bioinformatics 2001,17(2):115-25. CrossRef
  15. 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 CJJ, Brazma A: Design and implementation of microarray gene expression markup language (MAGE-ML). / Genome Biol 2002,3(9):RESEARCH0046. CrossRef
  16. Jones AR, Paton NW: An analysis of extensible modelling for functional genomics data. / BMC Bioinformatics 2005, 6:235. CrossRef
  17. PSI-MS[http://psidev.sourceforge.net/ms/ ]
  18. Matrix Science[http://www.matrixscience.com/ ]
  19. JHUPO[http://www1.biz.biglobe.ne.jp/~jhupo/index-e.htm ]
  20. DSTC[http://titanium.dstc.edu.au/xml/xmldbgui/ ]
  
• 作者单位：Feng Li (1) (2)
  Maoyu Li (1)
  Zhiqiang Xiao (1)
  Pengfei Zhang (1)
  Jianling Li (1)
  Zhuchu Chen (1) (2)
  
  1. Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
  2. Cancer Research Institute, Central South University, Changsha, China
  
• ISSN：1471-2105

文摘

Background Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. Results The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Conclusion Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.