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ms-data-core-api specifications


Unique identifier OMICS_08588
Name ms-data-core-api
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Juan Antonio VizcaĆ­no

Publication for ms-data-core-api

ms-data-core-api citations


The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Genome Biol
PMCID: 5793360
PMID: 29386051
DOI: 10.1186/s13059-017-1377-x

[…] and proBed, although it should be noted that the representation for proteogenomics data in mzIdentML has only been formalized recently []. In this context, first of all, the open-source Java library ms-data-core-api, created to handle different proteomics file formats using the same interface, can be used to write proBed []. A Java command line tool, PGConverter ( […]


Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] s, can be used to manipulate them. To convert existing MS-based proteomics identifications results in mzIdentML and mzTab format, among other formats, several tools have also recently been developed. ms-data-core-api and PGConverter ( write to proBed, proBAMr writes to proBAM, and proBAMconvert ( writes to both formats. PGConve […]


Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes

Cell Syst
PMCID: 5571441
PMID: 28837811
DOI: 10.1016/j.cels.2017.07.007

[…] pective genomic coordinates and color coded for the type of modification.A separate FileConverter implemented in java supports standardized PSI file formats such as mzIdentML and mzTab through use of ms-data-core-api. () Furthermore, the file converter is integrated into a java implemented graphical user interface (GUI) for PoGo enabling non-bioinformaticians to map peptides to reference genomes. […]


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ms-data-core-api institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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