jmz<scp>I</scp>dent<scp>ML API</scp>: A <scp>J</scp>ava interface to the mz<scp>I</scp>dent<scp>ML</scp> standard for peptide and protein identification data

Abstract

We present a J ava application programming interface ( API ), jmz I dent ML , for the Human Proteome Organisation ( HUPO ) Proteomics Standards Initiative ( PSI ) mz I dent ML standard for peptide and protein identification data. The API combines the power of J ava A rchitecture of XML B inding ( JAXB ) and an XP ath‐based random‐access indexer to allow a fast and efficient mapping of extensible markup language ( XML ) elements to J ava objects. The internal references in the mz I dent ML files are resolved in an on‐demand manner, where the whole file is accessed as a random‐access swap file, and only the relevant piece of XML is selected for mapping to its corresponding J ava object. The API is highly efficient in its memory usage and can handle files of arbitrary sizes. The API follows the official release of the mz I dent ML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/ .

Keywords

Affiliated Institutions

• European Bioinformatics Institute GB
• University of Liverpool GB
• Wellcome Trust GB

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