{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T05:01:01Z","timestamp":1761541261285},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":527,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: The software is freely available at https:\/\/github.com\/PRIDE-Utilities\/ms-data-core-api.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>\n               <jats:p>Contact: \u00a0juan@ebi.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv250","type":"journal-article","created":{"date-parts":[[2015,4,25]],"date-time":"2015-04-25T01:51:42Z","timestamp":1429926702000},"page":"2903-2905","source":"Crossref","is-referenced-by-count":29,"title":["ms-data-core-api: an open-source, metadata-oriented library for computational proteomics"],"prefix":"10.1093","volume":"31","author":[{"given":"Yasset","family":"Perez-Riverol","sequence":"first","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julian","family":"Uszkoreit","sequence":"additional","affiliation":[{"name":"2 Ruhr-Universit\u00e4t Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universit\u00e4tsstr. 150, D-44801 Bochum, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aniel","family":"Sanchez","sequence":"additional","affiliation":[{"name":"3 Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"Ternent","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noemi","family":"del Toro","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Antonio","family":"Vizca\u00edno","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Wang","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,4,24]]},"reference":[{"key":"2023020202222110400_btv250-B1","doi-asserted-by":"crossref","first-page":"2765","DOI":"10.1074\/mcp.O113.036681","article-title":"The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience","volume":"13","author":"Griss","year":"2014","journal-title":"Molecular & cellular proteomics: MCP"},{"key":"2023020202222110400_btv250-B2","doi-asserted-by":"crossref","first-page":"M111 014381","DOI":"10.1074\/mcp.M111.014381","article-title":"The mzIdentML data standard for mass spectrometry-based proteomics results","volume":"11","author":"Jones","year":"2012","journal-title":"Molecular & cellular proteomics: MCP"},{"key":"2023020202222110400_btv250-B3","doi-asserted-by":"crossref","first-page":"R110 000133","DOI":"10.1074\/mcp.R110.000133","article-title":"mzML\u2014a community standard for mass spectrometry data","volume":"10","author":"Martens","year":"2011","journal-title":"Mol. 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