The primary purpose of ms-data-core-api library is to provide commonly used classes and Object Model for Proteomics Experiments. You may also find it useful for your own computational proteomics projects.

• Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R. (2015). ms-data-core-api: An open-source, metadata-oriented library for computational proteomics. Bioinformatics. 2015 Apr 24. PDF File Pubmed Record

ms-data-core-api is a PRIDE API licensed under Apache License 2.0.

• Common Object Model for different proteomics experiments, with classes to represent proteins, peptides, psms, psectrums
• DataAccessControllers for mzTab, mzIdentML, PRIDE XML, PRIDE Database, mzML, mzXML, mgf, pkl, apl, ms2, dta files
• Proteomics Standard compleint Data model with classes for Ontologies and User params
• Read different file formats in proteomics in a common Object Model
• Export the current model to mzTab files in for Identification Experiments.

Note: the library is still evolving, we are committed to expand this library and add more useful classes.

The zip file in the releases section contains the ms-data-core-api jar file and all other required libraries.

Maven Dependency

PRIDE Utilities library can be used in Maven projects, you can include the following snippets in your Maven pom file.

<dependency>
  <groupId>uk.ac.ebi.pride.utilities</groupId>
  <artifactId>ms-data-core-api</artifactId>
  <version>x.x.x</version>
</dependency> 

<!-- EBI repo -->
<repository>
    <id>nexus-ebi-release-repo</id>
    <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
</repository>

<!-- EBI SNAPSHOT repo -->
<snapshotRepository>
   <id>nexus-ebi-snapshots-repo</id>
   <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
</snapshotRepository>

Note: you need to change the version number to the latest version.

For developers, the latest source code is available from our SVN repository.

If you have questions or need additional help, please contact the PRIDE Helpdesk at the EBI: pride-support at ebi.ac.uk (replace at with @).

Please send us your feedback, including error reports, improvement suggestions, new feature requests and any other things you might want to suggest to the PRIDE team.

• Wang, R., Fabregat, A., Ríos, D., Ovelleiro, D., Foster, J. M., Côté, R. G., ... & Vizcaíno, J. A. (2012). PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nature biotechnology, 30(2), 135-137. PDF File, Pubmed Record
• Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., ... & Hermjakob, H. (2013). The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic acids research, 41(D1), D1063-D1069. PRIDE-Archive

This example shows how to read an mzIdentML file and retrieve the information from them:

//Open an inputFile mzIdentml File using memory 
MzIdentMLControllerImpl mzIdentMlController = new MzIdentMLControllerImpl(inputFile, true);

//Print size of the Sample List
List<Sample> samples = mzIdentMlController.getSamples();
System.out.println(samples.size());

//Print the Id of the first sample
System.out.println(samples.get(0).getId());

//Print size of the Software List
System.out.println(software.size());

//Print the Name of the first Software
System.out.println(software.get(0).getName());

//Retrieve the Identification Metadata    
IdentificationMetaData experiment = mzIdentMlController.getIdentificationMetaData();
// test SearchDatabase
List<SearchDataBase> databases = experiment.getSearchDataBases();
        
// test SpectrumIdentificationProtocol
List<SpectrumIdentificationProtocol> spectrumIdentificationProtocol = experiment.getSpectrumIdentificationProtocols();

// Retrieve the Protein Identification Protocol
Protocol proteinDetectionProtocol = experiment.getProteinDetectionProtocol();

//Retrieve all Protein Identifications
List<Comparable> identifications = new ArrayList<Comparable>(mzIdentMlController.getProteinIds());

This example shows how to read an PRIDE XML file and retrieve the information from them:

//Open an inputFile mzIdentml File using memory 
PrideXmlControllerImpl prideXMLController = new PrideXmlControllerImpl(inputFile);

// You can use the example above and the same functions to retrieve the data using this controller for example:
//Print size of the Sample List
List<Sample> samples = prideXMLController.getSamples();
System.out.println(samples.size());