title: jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
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/.
authors.affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Ritesh
authors.initials: R
authors.lastname: Krishna
authors.forename: Fawaz
authors.initials: F
authors.lastname: Ghali
authors.forename: Daniel
authors.initials: D
authors.lastname: Ríos
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
mesh_terms: D000595:Amino Acid Sequence; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D012984:Software / Q000592:standards
chemical_list: D010455:Peptides; D011506:Proteins; D020543:Proteome