The project participants accessed the database through a web-based SQL interface developed specifically for project needs. During the data submission process, before the official in-project data release, each laboratory could retrieve only its own data submitted to date. After the in-project data release, laboratories could freely access data from all the participants. The database access was limited to the project laboratories by a user and password mechanism. Each laboratory could use a set of predefined SQL queries to perform standard data requests as well as define its own, private queries for more specific tasks and save these for future use.
For the dissemination of the data gathered by the HUPO-PPP, the ab initio construction of a novel data structure was decided upon. Indeed, the PPP, as the first HUPO project to complete the pilot milestone, is uniquely positioned for fulfilling the pioneering role in establishing such a data (infra) structure. The finalized data are publicly available in the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/ pride) (see Martens et al., this issue). The results of a PRIDE web query can be visualized either as an HTML page or in the PRIDE XML format. The complete PRIDE database is also available for download in XM L format. The PRIDE project site offers an Application Programmers Interface (API), which provides the tools necessary to efficiently access the PRIDE XML format and reference database implementation programmatically.
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