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


CONCLUSIONS
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/.
Li
Feng
F
Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China. fengl@xysm.net
Li
Maoyu
M
Xiao
Zhiqiang
Z
Zhang
Pengfei
P
Li
Jianling
J
Chen
Zhuchu
Z
D002277:Carcinoma / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D016678:Genome; D006801:Humans; D019146:Hypermedia; D016247:Information Storage and Retrieval; D007256:Information Systems; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D009303:Nasopharyngeal Neoplasms / Q000378:metabolism*; D011381:Programming Languages; D040901:Proteomics; D012984:Software; D012985:Software Design; D014584:User-Computer Interface