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

2012; Wiley; Volume: 12; Issue: 6 Linguagem: Inglês

10.1002/pmic.201100577

1615-9861

Florian Reisinger, Ritesh Krishna, Fawaz Ghali, Daniel Ríos, Henning Hermjakob, Juan Antonio Vizcaíno, Andrew R. Jones,

Mass Spectrometry Techniques and Applications

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/ .