Java API for MIAPE Generation

- DE, http://www.ebi.ac.uk/pride) has become one of the main repositories of mass spectrometry derived proteomics data. In this communication we will summarize the main capabilities of the PRIDE sys- tem, including its associated tools. Finally, we will introduce the ProteomeXchange consortium, as a collaborative approach to share proteomics data bet- ween the most important proteomics repositories. (http://www.ebi.ac.uk/pride) at the European Bio- informatics Institute (EBI) provides users with the ability to explore and compare mass spectrometry (MS) based proteomics experiments that reveal de- tails of the protein expression found in a broad range of taxonomic groups, tissues and disease states [1]. PRIDE stores three different kinds of information: or MS/MS experiments, MS and MS/MS mass spec- tra as peak lists, and any and all associated metadata. PRIDE is now the recommended submission point for proteomics data for several journals such as Na- ture Biotechnology, Nature Methods, Molecular and Cellular Proteomics, and Proteomics. 1. PRIDE associated tools PRIDE relies heavily on two additional tools: the Ontology Lookup Service [2] (OLS, http://www. ProteomeXchange consortium Juan Antonio Vizcaino, Florian Reisinger, Richard Cote, Henning Hermjakob ebi.ac.uk/ols - ferencing system [3] (PICR, http://www.ebi.ac.uk/ Tools/picr). OLS provides convenient and powerful access to a large number of biomedical ontologies and controlled vocabularies (CVs). PRIDE takes advantage of OLS to store, structure, and present any and all metadata annotations on experiments, proteins, peptides and mass spectra. The PICR tool on the other hand, is built to over- come one of the most recurrent problems in proteo- mics: the existence of heterogeneous and changing protein in different databases. PICR is used to map to all known accession numbers for those proteins in the most important protein databases (including UniProt, IPI, Ensembl and RefSeq, among others). originally derived from different databases, or from different time points of the same database, thus be- come fully comparable. In addition to these two es- tablished tools, a new application called Database on Demand [4] (DoD, http://www.ebi.ac.uk/pride/dod) has recently been added to the PRIDE toolkit. This tool allows custom sequence databases to be built in order to optimize the results from search engines for gel-free proteomics experiments. 2. ProteomeXchange Consortium One of the reasons why proteomics data sharing is not a universal fact yet is the heterogeneity of the