ms-data-core-api | Datasets2Tools

General Information

Description	An open-source, metadata-oriented library for computational proteomics
Homepage	https://github.com/PRIDE-Utilities/ms-data-core-api

Publications

Bioinformatics (2015)

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

Yasset Perez-Riverol; Julian Uszkoreit; Aniel Sanchez; Tobias Ternent; Noemi del Toro; Henning Hermjakob; Juan Antonio Vizcaíno; Rui Wang

Summary: The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library.

Availability and implementation: The software is freely available at https://github.com/PRIDE-Utilities/ms-data-core-api.

Supplementary information: Supplementary data are available at Bioinformatics online

Contact: juan@ebi.ac.uk

DOI: https://doi.org/10.1093/bioinformatics/btv250

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