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.
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.
This example shows how to read an mzIdentML file and retrieve the information from them:
import uk.ac.ebi.pride.utilities.data.core.*;
//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());
// Get the list of softwares from the mzIdentMlController
List<Software> software = mzIdentMlController.getSoftwares();
//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());
Convert from mzIdentML to mzTab
java -jar ms-data-core-api<version>.jar -c -mzid <input.mzid> -outputfile <output.mztab>
Convert from PRIDE XML to mzTab
java -jar ms-data-core-api<version>.jar -c -pridexml <pride.xml> -outputformat <output.mztab>
Convert from annotated mzTab to (sorted, filtered*) proBed
java -jar ms-data-core-api<version>.jar -c -mztab <input.mztab> -chromsizes <chrom.txt> -outputformat probed
Convert from annotated mzIdentML to (sorted, filtered*) proBed
java -jar ms-data-core-api<version>.jar -c -mzid <input.mztab> -chromsizes <chrom.txt> -outputformat probed
Convert from (sorted, filtered*) proBed to bigBed
java -jar ms-data-core-api<version>.jar -c -mztab <input.pro.bed> -chromsizes <chrom.txt> -asqlfile <aSQL.as> -bigbedconverter <bedToBigBed>
MzIdentML validation
java -jar ms-data-core-api<version>.jar -v -mzid <sample.mzid> -peak <spectra.mgf> -skipserialization -reportfile <outputReport.txt>
MzTab validation
java -jar ms-data-core-api<version>.jar -v -mztab <input.mztab> -peaks <spectra1.mgf>##<spectra2.mgf> -skipserialization -reportfile <outputReport.txt>
PRIDE XML validation
java -jar ms-data-core-api<version>.jar -v -pridexml <input.pride.xml> -skipserialization -reportfile <outputReport.txt>
MzIdentML schema validation and normal validation
java -jar ms-data-core-api<version>.jar -v -mzid <input.mzid> -peak <spectra.mgf> -scehma -skipserialization -reportfile <outputReport.txt>
PRIDE XML schema validation only, without normal validation
java -jar ms-data-core-api<version>.jar -v -pridexml <input.pride.xml> -schemaonly -skipserialization -reportfile <outputReport.txt>
ProBed validation with the default schema
java -jar ms-data-core-api<version>.jar -v -proBed <input.pro.bed> -reportfile <outputReport.txt>
ProBed validation with a custom schema
java -jar ms-data-core-api<version>.jar -v -proBed -proBed <input.pro.bed> -asqlfile <input.as> -reportfile <outputReport.txt>
Check Results Files
java -jar ms-data-core-api<version>.jar -check -inputfile <inputfile>
Convert PRIDE or mzIdentML file to MzTab
java -jar ms-data-core-api<version>.jar -convert -inputfile <inputfile> -format <format>
Print Error/Warn detail message based on code
java -jar ms-data-core-api<version>.jar -error -code <code>
Help
java -jar ms-data-core-api<version>.jar -h or --help
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.
ms-data-core-api is a PRIDE API licensed under Apache License 2.0.