jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data |
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Authors: | Reisinger Florian Krishna Ritesh Ghali Fawaz Ríos Daniel Hermjakob Henning Vizcaíno Juan Antonio Jones Andrew R |
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Institution: | EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. |
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Abstract: | We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML 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 XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. |
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Keywords: | Bioinformatics Java API mzIdentML Proteomics standards initiative (PSI) XML |
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