Abstract
BackgroundMany 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.ResultsThe 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.ConclusionOur 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 .
Highlights
Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results
One Nasopharyngeal carcinoma (NPC) 2D/MS repository query result displayed in Internet Explore without transforming with Sablotron XSLT processor
Complicated data structure in the proteomics data integrated with Human Proteome Markup Language (HUP-ML) model makes it difficulty to construct a proteomics repository with RDBMS because of some problems in mapping hierarchical structure to relational schema
Summary
Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. 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. All cells contain the complete genome, only a fraction of the genes are expressed within a given cell. The term 'proteome' is a hybrid of "PROTEin" and "genOME" and it refers to the entire protein components, along with all covalent protein modifications in a selected cell. One NPC 2D/MS repository query result displayed in Internet Explore without transforming with Sablotron XSLT processor. The root of the query result XML document was result tag. Every query record would be inserted among spot tag
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