publication . Article . 2012

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

Andrew Jones; Fawaz Ghali; Juan Antonio Vizcaíno; Henning Hermjakob;
Open Access English
  • Published: 01 Jan 2012 Journal: PROTEOMICS, volume 12, issue 6, pages 790-794 (issn: 1615-9853, Copyright policy)
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 ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Technical Brief, Bioinformatics, Java API, mzIdentML, Proteomics standards initiative (PSI), XML
Funded by
RCUK| Standards-compliant software tools for curation and public deposition of proteomics data
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/H024654/1
  • Funding stream: BBSRC
,
WT| The Proteomics Identifications Database (PRIDE).
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 085949
  • Funding stream: Cellular and Molecular Neuroscience
,
EC| PROTEOMEXCHANGE
Project
PROTEOMEXCHANGE
International Data Exchange and Data Representation Standards for Proteomics
  • Funder: European Commission (EC)
  • Project Code: 260558
  • Funding stream: FP7 | SP1 | HEALTH
,
EC| LIPIDOMICNET
Project
LIPIDOMICNET
Lipid droplets as dynamic organelles of fat deposition and release: Translational research towards human disease
  • Funder: European Commission (EC)
  • Project Code: 202272
  • Funding stream: FP7 | SP1 | HEALTH
,
RCUK| Developing proteome-bioinformatics methods for a large scale refinement of gene models in Apicomplexan parasites
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/G010781/1
  • Funding stream: BBSRC

DC, Wedge, R, Krishna, P, Blackhurst, JA, Siepen. FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J. Proteome. Res. 2011; 10: 2088-2094 [OpenAIRE] [PubMed]

M, Sturm, A, Bertsch, C, Gropl, A, Hildebrandt. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008; 9-163

D, Kessner, M, Chambers, R, Burke, D, Agus. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008; 24: 2534-2536 [OpenAIRE] [PubMed]

H, Barsnes, S, Huber, A, Sickmann, I, Eidhammer. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MSsearch results. Proteomics. 2009; 9: 3772-3774 [PubMed]

T, Muth, M, Vaudel, H, Barsnes, L, Martens. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 2010; 10: 1522-1524 [OpenAIRE] [PubMed]

H, Barsnes, JA, Vizcaino, I, Eidhammer, L, Martens. PRIDE Converter: making proteomics data-sharing easy. Nat. Biotechnol.. 2009; 27: 598-599 [OpenAIRE] [PubMed]

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 ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Technical Brief, Bioinformatics, Java API, mzIdentML, Proteomics standards initiative (PSI), XML
Funded by
RCUK| Standards-compliant software tools for curation and public deposition of proteomics data
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/H024654/1
  • Funding stream: BBSRC
,
WT| The Proteomics Identifications Database (PRIDE).
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 085949
  • Funding stream: Cellular and Molecular Neuroscience
,
EC| PROTEOMEXCHANGE
Project
PROTEOMEXCHANGE
International Data Exchange and Data Representation Standards for Proteomics
  • Funder: European Commission (EC)
  • Project Code: 260558
  • Funding stream: FP7 | SP1 | HEALTH
,
EC| LIPIDOMICNET
Project
LIPIDOMICNET
Lipid droplets as dynamic organelles of fat deposition and release: Translational research towards human disease
  • Funder: European Commission (EC)
  • Project Code: 202272
  • Funding stream: FP7 | SP1 | HEALTH
,
RCUK| Developing proteome-bioinformatics methods for a large scale refinement of gene models in Apicomplexan parasites
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/G010781/1
  • Funding stream: BBSRC

DC, Wedge, R, Krishna, P, Blackhurst, JA, Siepen. FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J. Proteome. Res. 2011; 10: 2088-2094 [OpenAIRE] [PubMed]

M, Sturm, A, Bertsch, C, Gropl, A, Hildebrandt. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008; 9-163

D, Kessner, M, Chambers, R, Burke, D, Agus. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008; 24: 2534-2536 [OpenAIRE] [PubMed]

H, Barsnes, S, Huber, A, Sickmann, I, Eidhammer. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MSsearch results. Proteomics. 2009; 9: 3772-3774 [PubMed]

T, Muth, M, Vaudel, H, Barsnes, L, Martens. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 2010; 10: 1522-1524 [OpenAIRE] [PubMed]

H, Barsnes, JA, Vizcaino, I, Eidhammer, L, Martens. PRIDE Converter: making proteomics data-sharing easy. Nat. Biotechnol.. 2009; 27: 598-599 [OpenAIRE] [PubMed]

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